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Commit 04601824 authored by Bertjan Broeksema's avatar Bertjan Broeksema
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Remove all files from gh-pages branch to add documentation

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^.*\.Rproj$
^\.Rproj\.user$
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^.*\.Rproj$
^\.Rproj\.user$
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.Rproj.user
.Rhistory
.RData
*.swp
data.raw/*
data/*
.idea/*
inst/www/node_modules
cstr.db
/rScratch
R.ICoVeR/DESCRIPTION deleted 100644 → 0
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Package: ICoVeR
Type: Package
Title: An application for interactive binning of contigs and bin refinement
Version: 0.1.0
Date: 2015-06-11
Author: Bertjan Broeksema <research@broeksemaatjes.nl>
Maintainer: Bertjan Broeksema <research@broeksemaatjes.nl>
Description: An application for interactive binning of contigs and bin refinement.
License: GPLv3
LazyData: true
Depends: FactoMineR, RSQLite, Hmisc, ca
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Version: 1.0
RestoreWorkspace: No
SaveWorkspace: No
AlwaysSaveHistory: Yes
EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: UTF-8
RnwWeave: Sweave
LaTeX: pdfLaTeX
AutoAppendNewline: Yes
StripTrailingWhitespace: Yes
BuildType: Package
PackageUseDevtools: Yes
PackageInstallArgs: --no-multiarch --with-keep.source
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NPM := $(shell which npm)
JSLINT := $(shell which jslint)
SRC_DIR := inst/www
JS_MODULES := js js/controllers js/services js/templates
JS_SRC_DIR := $(addprefix $(SRC_DIR)/, $(JS_MODULES))
JS_SRC := $(foreach srcdir, $(JS_SRC_DIR), $(wildcard $(srcdir)/*.js))
# All must be the first target so that it is run automatically when you run make
# without a target specified.
all: init
npm:
ifdef NPM
@which npm > /dev/null
else
@echo "* Please install npm before continuing..."
@which npm > /dev/null
endif
jslint: npm
ifdef JSLINT
@which jslint > /dev/null
else
@echo "* Please install jslint before continuing..."
@echo " - e.g. try npm install jslint -g"
@which jslint > /dev/null
endif
.git/hooks/pre-commit: git-hooks/pre-commit
@echo " - pre-commit"
@cp git-hooks/pre-commit .git/hooks
@chmod +x .git/hooks/pre-commit
githooks: .git/hooks/pre-commit
init: jslint githooks
check: $(JS_SRC)
@jslint --edition=2014-07-08 $^
.PHONY: githooks init check
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exportPattern("^data\\.[[:alpha:]]*")
exportPattern("^cluster\\.[[:alpha:]]*")
exportPattern("^dimred\\.[[:alpha:]]*")
exportPattern("^color\\.[[:alpha:]]*")
exportPattern("^db\\.[[:alpha:]]*")
export("app.init")
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# ICoVeR - Interactive Contig-bin Verification and Refinement
#
# Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# cluster.kmeans(vars=c("M4", "M20", "M28", "M36", "M40", "M44", "M48"), identifier="kmeans_30_7", centers=30)
cluster.kmeans <- function(rows = c(), vars, identifier, centers = NA, iter.max=10) {
clusterData <- data.get(rows, vars)
clusterRows <- clusterData$row
clusterData$row <- NULL
if (is.na(centers)) centers <- floor(sqrt(nrow(clusterData)))
clusters <- as.factor(stats::kmeans(clusterData, centers, iter.max)$cluster)
clusters <- data.frame(row = clusterRows, cluster = clusters)
p.db.extend.schema(name = identifier, type = "factor", group = "Analytics",
group_type = "Clusterings")
p.db.add.column(column.name = identifier, type = "integer")
lapply(levels(clusters$cluster), function(level) {
level <- as.numeric(level)
rows <- clusters$row[clusters$cluster==level]
p.db.store(column.name = identifier, rows = rows, value = level)
})
}
cluster.correlation <- function(rows = c(), vars, identifier,
pearsonThreshold = 0.9, minClusterSize=2) {
# Get the data to cluster and keep track of row numbers.
clusterData <- data.get(rows, vars)
rownames(clusterData) <- clusterData$row
# Make sure that the row number is not included in the clustering process
clusterData$row <- NULL
Corrclusters <- as.data.frame(correlationCluster(clusterData))
Corrclusters$cluster <- as.factor(Corrclusters$cluster)
# Add a new column to the schema and the data table to store the new
# clustering variable into.
p.db.extend.schema(name = identifier, type = "factor", group = "Analytics",
group_type = "Clusterings")
p.db.add.column(column.name = identifier, type = "integer")
# Now, store the clustering levels for each row in the data base per level
lapply(levels(Corrclusters$cluster), function(level) {
rows <- Corrclusters$row[Corrclusters$cluster == level]
p.db.store(column.name = identifier, rows = rows, value = level)
})
TRUE
}
p.cluster.methods <- function() {
list("kmeans" = list(
"man" = "/ocpu/library/stats/man/kmeans/text",
"args" = list(
"identifier" = list("type" = "character", "required" = T),
"vars" = list("type"="schema.numeric", "required"=T),
"centers" = list("type"="numeric", "required"=F),
"iter.max" = list("type"="numeric", "required"=F, "default"=10),
"nstart" = list("type"="numeric", "required"=F, default=1),
"algorithm" = list("type"="character", "required"=F,
"values"=c("Hartigan-Wong", "Lloyd", "Forgy", "MacQueen"))
)
),
"correlation" = list(
"man" = "/ocpu/library/stats/man/kmeans/text",
"args" = list(
"identifier" = list("type" = "character", "required" = T),
"vars" = list("type"="schema.numeric", "required"=T),
"pearsonThreshold" = list("type"="numeric", "required"=F),
"minClusterSize" = list("type"="numeric", "required"=F, "default"=2)
)
)
)
}
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# ICoVeR - Interactive Contig-bin Verification and Refinement
#
# Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
library(Hmisc)
# This function takes a row profile (abundance change over time) x and a pearson
# correlation coefficient (PCC) threshold, and returns a function that can be
# applied to the full data set in order to find other contigs that are within
# the given PCC threshold.
hasStrongCorrelation <- function(x, pearson) {
function (y) {
above <- Hmisc::rcorr(as.double(x), as.double(y))$r[1,2] > pearson
if (is.na(above)) {
above <- FALSE
}
above
}
}
# This function takes a contig data set X and returns a boolean vector, which
# contains TRUE for each contig is within the given pearsonThreshold.
withinDistance <- function(X, pearsonThreshold) {
test <- hasStrongCorrelation(X[1, ], pearsonThreshold)
apply(X, 1, test)
}
clusterProfiles <- function(X, pearsonThreshold = .9, minClusterSize = 2) {
clustered <- NULL
clusterId <- 1
repeat {
correlates <- withinDistance(X, pearsonThreshold)
nextcluster <- X[correlates, ]
if (sum(correlates) > minClusterSize) {
nextcluster$cacId <- rep(clusterId, nrow(nextcluster))
clusterId <- clusterId + 1
} else {
nextcluster$cacId <- rep(-1, nrow(nextcluster))
}
clustered <- rbind(clustered, nextcluster)
if (sum(!correlates) < nrow(X)) {
X <- X[!correlates,]
} else { # None of the remaining rows correlates with one another.
X$cacId <- rep(-1, nrow(X))
clustered <- rbind(clustered, X)
break
}
if (nrow(X) == 0) {
break # None remaining rows left
}
}
clustered
}
correlationCluster <- function(X, pearsonThreshold = .9, minClusterSize = 2) {
# First step, cluster profiles based on pearsonThreshold
clustered <- clusterProfiles(X, pearsonThreshold, minClusterSize)
# Deal with the case that no items where clustered together, because no two
# items had a correlatation >= pearsonThreshold
if (sum(clustered$cacId) == nrow(clustered) * -1) {
clustering <- cbind(as.integer(rownames(clustered)), -1)
colnames(clustering) <- c("row", "cluster")
return(clustering)
}
# Next step: merge clusters based on average profiles and PCC.
# For this we only look at the data that have a cluster ID != -1, because -1
# represents data with no strong correlations among each other.
repeat {
clusterMeans <- clustered[clustered$cacId != -1, ]
clusterMeans <- aggregate(clusterMeans, list(cacId = clusterMeans$cacId), mean)
clusterId <- 1
mergeCount <- 0 # Incremented when 2 or more clusters are merged
repeat {
correlates <- withinDistance(clusterMeans, .97) # .97 From Nielsen et al.
clusterIds <- clusterMeans[correlates, ]$cacId
#print(clusterIds)
# Reassign cluster ids
clustered[clustered$cacId %in% clusterIds, ]$cacId <- clusterId
clusterId <- clusterId + 1
if (length(clusterIds) > 1) {
mergeCount <- mergeCount + 1
}
clusterMeans <- clusterMeans[!correlates,]
if (nrow(clusterMeans) == 0) break
}
if (mergeCount == 0) break
}
clustering <- cbind(as.integer(rownames(clustered)), clustered$cacId)
colnames(clustering) <- c("row", "cluster")
clustering
}
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# ICoVeR - Interactive Contig-bin Verification and Refinement
#
# Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
data.schema <- function(timestamp = Sys.time()) {
p.db.select(table="schema")
}
# data.get(rows = c(1,2,3,5,10), variables = c("gc_content"))
# data.get(variables = c("gc_content"))
data.get <- function(rows = c(), variables, addRows=T) {
if (addRows) variables <- c("row", variables)
data <- p.db.select(table="data", vars=variables, rows=rows)
factorVariables <- p.db.types(variables)
factorVariables <- factorVariables[factorVariables$type == "factor", c('name')]
Map(function(variable) {
data[variable] <<- as.factor(unlist(data[variable]))
}, factorVariables);
data
}
data.addTag <- function(timestamp, name, data) {
p.db.extend.schema(name = name, type = "boolean", group = "Tags", group_type = "Tags")
p.db.add.column(column.name = name, type = "integer")
p.db.store(column.name = name, rows = which(data==0), value = 0)
p.db.store(column.name = name, rows = which(data==1), value = 1)
}
data.removeTag <- function(timestamp, name) {
p.db.truncate.schema(name = name)
p.db.remove.column(column.name = name)
}
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# ICoVeR - Interactive Contig-bin Verification and Refinement
#
# Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
p.dimred.methods <- function() {
list(
"pca" = list(
"restrict" = list("type"="schema.numeric", "group_type"="!Frequencies")
),
"ca" = list(
"restrict" = list("type"="schema.numeric", "group_type"="Frequencies")
),
"mca" = list(
"restrict" = list("type"="schema.factor", "group_type"="Characteristics")
)
)
}
p.dataAndLabels <- function(rows, vars) {
# Make sure to also retrieve the names of the individuals
ids <- subset(data.schema(), group_type == "Id");
idName <- NULL
if (nrow(ids) > 0) {
idName <- ids[1,]$name
vars <- c(vars, idName)
}
# Get the actual data
data <- data.get(rows, vars, addRows=T)
# Remove the labels from the data as we do not want them analysed
if (!is.null(idName)) {
labels <- data[[idName]]
data[[idName]] <- NULL
} else {
labels <- NULL
}
# The database calls the column with row names "row" instead of R's "row.names"
rownames(data) <- data$row
data$row <- NULL
return(list(data = data, labels = labels))
}
p.projections <- function(dim.red.res, column.results) {
# marge.row and marge.col are respectively the masses for the rows and the columns
weightName <- "marge.row"
if (column.results == "var" || column.results == "col") {
weightName <- "marge.col"
}
factors <- 1:(ncol(dim.red.res[[column.results]]$coord))
projections <- data.frame(matrix(NA, nrow=nrow(dim.red.res[[column.results]]$coord), ncol=4))
projections$id <- rownames(dim.red.res[[column.results]]$coord)
projections$mass <- dim.red.res$call[[weightName]]
projections$coord <- dim.red.res[[column.results]]$coord[, factors]
projections$contrib <- dim.red.res[[column.results]]$contrib[, factors]
# We do not use the official rownames as the label tag is a bit friendlier
rownames(projections) <- NULL
projections
}
p.generate.structure <- function(processedData, individualProjections, variableProjections, explainedVariance, method) {
# We send processedData as a matrix, to make the JSON smaller and computations in the front-end faster
processedList <- list(
rowNames = rownames(processedData),
columnNames = colnames(processedData),
data = data.matrix(processedData)
)
list(
processedData = processedList,
individualProjections = individualProjections,
variableProjections = variableProjections,
explainedVariance = explainedVariance,
method = method
)
}
p.plotdata <- function(dim.red.res, labels, processedData, type) {
varName <- "var"
indName <- "ind"
if (type == "ca") {
varName <- "col"
indName <- "row"
}
# If we have a large number of individuals the JSON will be too big and the visualisation will fail.
# TODO: fine-tune the 2500 individuals threshold
individualProjections <- NULL
includeIndividuals <- nrow(dim.red.res[[indName]]$coord) < 2500
if (includeIndividuals) {
individualProjections <- p.projections(dim.red.res, column.results = indName)
if (!is.null(labels)) {
individualProjections$label <- labels
}
}
# TODO: optimise processedData storage, currently it is a data.frame,
# which means that every column name is present in every row
analysis <- p.generate.structure(
processedData = processedData,
individualProjections = individualProjections,
variableProjections = p.projections(dim.red.res, column.results = varName),
explainedVariance = dim.red.res$eig$"percentage of variance",
method = type
)
if (!includeIndividuals) {
analysis$individualProjections <- NULL
}
analysis
}
# dimred.pca(vars = c("M4", "M20", "M28", "M36", "M40", "M44", "M48"))
dimred.pca <- function(rows=c(), vars) {
res <- p.dataAndLabels(rows, vars)
data <- res$data
# Create a dataframe with normalised data, to be used for the calculation of influence
columnNorms <- apply(data, 2, function(x){sqrt(sum(x^2))})
processedData <- as.data.frame(t(t(data)/columnNorms))
colnames(processedData) <- colnames(data)
rownames(processedData) <- rownames(data)
p.plotdata(FactoMineR::PCA(data, ncp=length(vars), graph=F), labels = res$labels, processedData = processedData, type = "pca")
}
# dimred.ca(vars=c("aaaa","aaac","aaag","aaat","aaca","aacc","aacg","aact","aaga","aagc","aagg","aagt","aata","aatc","aatg","aatt","acaa","acac","acag","acat","acca","accc","accg","acct","acga","acgc","acgg","acgt","acta","actc","actg","actt","agaa","agac","agag","agat","agca","agcc","agcg","agct","agga","aggc","aggg","aggt","agta","agtc","agtg","agtt","ataa","atac","atag","atat","atca","atcc","atcg","atct","atga","atgc","atgg","atgt","atta","attc","attg","attt","caaa","caac","caag","caat","caca","cacc","cacg","cact","caga","cagc","cagg","cagt","cata","catc","catg","catt","ccaa","ccac","ccag","ccat","ccca","cccc","cccg","ccct","ccga","ccgc","ccgg","ccgt","ccta","cctc","cctg","cctt","cgaa","cgac","cgag","cgat","cgca","cgcc","cgcg","cgct","cgga","cggc","cggg","cggt","cgta","cgtc","cgtg","cgtt","ctaa","ctac","ctag","ctat","ctca","ctcc","ctcg","ctct","ctga","ctgc","ctgg","ctgt","ctta","cttc","cttg","cttt"))
# dimred.ca(rows=c(19, 33, 36, 75, 81, 118, 169, 203, 218, 234, 236, 299, 380, 449, 457, 570, 572, 575, 579, 594, 595, 647, 679, 724, 736, 763, 764, 820, 833, 837, 1000, 1043, 1119, 1170, 1306, 1492, 1564, 1729, 1832, 1895, 2329, 2369, 2629, 2853, 3006, 3010, 3309, 3513, 3833, 5691, 6382, 6905, 7890, 10252, 13658), vars=c("aaaa","aaac","aaag","aaat","aaca","aacc","aacg","aact","aaga","aagc","aagg","aagt","aata","aatc","aatg","aatt","acaa","acac","acag","acat","acca","accc","accg","acct","acga","acgc","acgg","acgt","acta","actc","actg","actt","agaa","agac","agag","agat","agca","agcc","agcg","agct","agga","aggc","aggg","aggt","agta","agtc","agtg","agtt","ataa","atac","atag","atat","atca","atcc","atcg","atct","atga","atgc","atgg","atgt","atta","attc","attg","attt","caaa","caac","caag","caat","caca","cacc","cacg","cact","caga","cagc","cagg","cagt","cata","catc","catg","catt","ccaa","ccac","ccag","ccat","ccca","cccc","cccg","ccct","ccga","ccgc","ccgg","ccgt","ccta","cctc","cctg","cctt","cgaa","cgac","cgag","cgat","cgca","cgcc","cgcg","cgct","cgga","cggc","cggg","cggt","cgta","cgtc","cgtg","cgtt","ctaa","ctac","ctag","ctat","ctca","ctcc","ctcg","ctct","ctga","ctgc","ctgg","ctgt","ctta","cttc","cttg","cttt"))
dimred.ca <- function(rows=c(), vars) {
# TODO: Instead of this matrix use the burt matrix where rows represent
# columns as well. It must be something ling: data x data^T. Its size
# is number of cols X number of cols. It should make the operation.
res <- p.dataAndLabels(rows, vars)
data <- res$data
CAres <- FactoMineR::CA(data, ncp=length(vars), graph=F)
# CAres$call$X contains the normalised data
processedData <- CAres$call$X
p.plotdata(CAres, labels = res$labels, processedData = processedData, type = "ca")
}
# Processes the result of a ca::mjca analysis, we pass nd along because mjca ignores
# the parameter and gives us too many dimensions
p.mca.plotdata <- function(dim.red.res, labels, processedData, nd) {
variableProjections <- data.frame(matrix(NA, nrow=nrow(dim.red.res$colcoord), ncol=4))
variableProjections$id <- dim.red.res$levelnames
variableProjections$mass <- dim.red.res$colmass
variableProjections$coord <- dim.red.res$colcoord[,1:nd]
variableProjections$contrib <- dim.red.res$colctr[,1:nd]
individualProjections <- data.frame(matrix(NA, nrow=nrow(dim.red.res$rowcoord), ncol=4))
individualProjections$id <- rownames(processedData)
individualProjections$mass <- rep(1 / nrow(processedData), nrow(processedData))
individualProjections$coord <- dim.red.res$rowcoord[,1:nd]
individualProjections$contrib <- dim.red.res$rowcoord[,1:nd]^2
if (!is.null(labels)) {
individualProjections$label <- labels
}
# If we have a large number of individuals the JSON will be too big and the visualisation will fail.
# TODO: fine-tune the 2500 individuals threshold
includeIndividuals <- nrow(processedData) < 2500
if (!includeIndividuals) {
individualProjections <- NULL
}
# TODO: optimise processedData storage, currently it is a data.frame,
# which means that every column name is present in every row
analysis <- p.generate.structure(
processedData = processedData,
variableProjections = variableProjections,
individualProjections = individualProjections,
explainedVariance = dim.red.res$inertia.e[1:nd] * 100,
method = "mca"
)
if (!includeIndividuals) {
analysis$individualProjections <- NULL
}
analysis
}
#dimred.mca(vars=c("Exposition", "Max_Lithol", "Max_Permea", "Max_Zumste", "climatic_class", "Geologie", "Soil", "Bodenzustand", "GrAndigkeit", "Lage_im_Relief", "Durchwurzelung", "WAlbung", "Tiefe_cm_A", "Horizont_A", "Bodenart_A", "Bodenfarbe_A", "Zeilung", "Bodenpflegesystem", "Art_der_Begrunung", "Unterstockbodenpflege", "Festigkeit_A", "Tiefe_cm_B", "Horizont_B", "Bodenart_B", "Bodenfarbe_B", "Festigkeit_B", "Unterlage", "Klon", "Bodenart"))
dimred.mca <- function(rows=c(), vars) {
res <- p.dataAndLabels(rows, vars)
data <- res$data
# MJCA is used because it produces much nicer names for the generated variables
MCAres <- ca::mjca(data, nd = NA, lambda = "indicator", reti=TRUE)
# Prepare the binary matrix as processedData
MCAres$indmat <- as.data.frame(MCAres$indmat)
colnames(MCAres$indmat) <- MCAres$levelnames
rownames(MCAres$indmat) <- rownames(data)
# For some reason MJCA gives a lot of very small PC's, here we indicate how many we really want.
nd <- length(which(MCAres$inertia.e > 0.01))
p.mca.plotdata(MCAres, res$labels, MCAres$indmat, nd = nd)
}
# dimred.summarize(variableWeights=list(aaaa=c(6.0151, 7.0562), aaat=c(4.7641, 2.7563), aata=c(4.175, 0.851), aatt=c(4.4429, 2.0970), ataa=c(4.1547, 0.8407), atat=c(3.1881, 0.1051), atta=c(4.1958, 0.7357), attt=c(4.7248, 2.7704)))
dimred.summarize <- function(rows=c(), variableWeights, identifier) {
data <- data.get(rows, names(variableWeights), addRows=T)
vars <- names(variableWeights)
summary <- rep(0, nrow(data))
sapply(vars, function(variable) {
weights <- variableWeights[[variable]]
col <- data[variable]
summary <<- summary + weights[1] * col + weights[2] * col
})
# FIXME: apperently summary is a one-itme list. The item is equal to a column
# name (the first one?), the value of this item is a vector with the summary
# values. There must be more R-like ways to prevent this from happening.
summary <- as.list(summary[[1]])
#list items names are used as row identifiers
names(summary) <- data$row
p.db.extend.schema(name = identifier, type = "numeric", group = "Analytics",
group_type = "Summaries")
p.db.add.column(column.name = identifier, type = "REAL")
p.db.storeList(column.name = identifier, values = summary)
#summary
}
R.ICoVeR/R/init.R deleted 100644 → 0
View file @ f9ef00c0
# ICoVeR - Interactive Contig-bin Verification and Refinement
#
# Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
app.init <- function(timestamp = Sys.time()) {
# Makes sure that the database is initialized and returns the schema of the
# data, and all the required UI configuration bits.
db.init()
schema <- data.schema(timestamp = timestamp)
# The Essential Single Copy gene information is stored in ${p.db.dataset}.rda
data(list=list(paste(p.db.dataset, ".escg", sep="")))
escg <- .GlobalEnv[[paste(p.db.dataset, ".escg", sep="")]]
data = list(
schema = schema,
dimensions = list(rows = p.db.rowcount(table = "data"), cols = nrow(schema))
)
cluster <- p.cluster.methods()
dimred <- p.dimred.methods()
list(data = data, cluster = cluster, dimred = dimred, escg = escg)
}
R.ICoVeR/R/sqlite.R deleted 100644 → 0
View file @ f9ef00c0
# ICoVeR - Interactive Contig-bin Verification and Refinement
#
# Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
library(DBI)
library(RSQLite)
# Some private helper functions and variables (starting with p.db.)
# Change this variable to switch data sets. It is expected that the data
# directory contains the files:
# - ${p.db.dataset}.rda
# - ${p.db.dataset}.schema.rda
p.db.dataset <- "cstr"
# NOTE: The "cache" databse will be created as: /tmp/RParcoords/cache.db under
# linux. In order to make this work with the opencpu service a couple of
# things need to be done on linux:
# 1) Some apparmor rules need to be set enable the RParcoords plugin to
# create a cache. The file: /etc/apparmor.d/opencpu.d/custom needs the
# following lines:
#
# /tmp/ICoVeR/ rw,
# /tmp/ICoVeR/** rwkmix,
#
# 2) The OpenCPU cache service must be disabled. Rationale: opencpu
# assumes each function to be pure (which is a reasonable assumption).
# However, we update the schema table in the sqlite database, and as
# such two calls to data.schema() can yield different results. This
# doesn't happen when the opencpu cache is enabled, as it will cache
# results of a function for given parameter configuration.
#
# 3) Make sure that OpenCPU can write large enough files from R. To
# achieve this edit /etc/opencpu/server.conf:
#
# "rlimit.fsize": 1e9,
#
p.db.file.path <- paste(.Platform$file.sep, paste("tmp", "ICoVeR", sep=.Platform$file.sep), sep="")
p.db.file.name <- paste(p.db.file.path, paste(p.db.dataset, "cache.db", sep="-"), sep=.Platform$file.sep)
db.init <- function() {
if (!file.exists(p.db.file.name)) {
if (!file.exists(p.db.file.path)) {
dir.create(p.db.file.path, recursive = T)
}
data(list=list(p.db.dataset, paste(p.db.dataset, ".schema", sep="")))
mSchema <- .GlobalEnv[[paste(p.db.dataset, ".schema", sep="")]]
mData <- .GlobalEnv[[p.db.dataset]]
mData$row <- as.integer(1:nrow(mData))
con <- DBI::dbConnect(RSQLite::SQLite(), p.db.file.name)
stopifnot(DBI::dbWriteTable(con, "data", mData, row.names=F))
stopifnot(DBI::dbWriteTable(con, "schema", mSchema, row.names=F))
#create index by row to allow for faster lookup / updates
res <- DBI::dbSendQuery(con,"CREATE INDEX row_index ON data (row ASC);")
DBI::dbClearResult(res)
DBI::dbDisconnect(con)
}
}
# This function makes sure column names are suitable for sqlite. It also prevents SQL injection.
p.db.escape.name <- function (name) {
name <- paste("\"", name, "\"", sep="")
}
p.db.connection <-function() {
DBI::dbConnect(RSQLite::SQLite(), p.db.file.name)
}
p.db.rowcount <- function(table) {
q <- paste("SELECT COUNT(*) FROM", table, sep=" ")
con <- p.db.connection()
rowcount <- DBI::dbGetQuery(con, q)
DBI::dbDisconnect(con)
as.vector(unlist(rowcount))
}
p.db.check.column.type <- function(type) {
type <- toupper(type)
if (!(type %in% c("INTEGER", "REAL", "TEXT"))) {
stop(paste("db.check.column.type - Invalid column type:", type))
}
type
}
# p.db.add.column(column.name="kmeans_35_M4", type="integer")
p.db.add.column <- function(table="data", column.name, type) {
type <- p.db.check.column.type(type)
con <- p.db.connection()
if (!(column.name %in% DBI::dbListFields(con, table))) {
column.name <- p.db.escape.name(column.name)
q <- paste("ALTER TABLE", table, "ADD COLUMN", column.name, type, sep=" ")
res <- DBI::dbSendQuery(con, q)
DBI::dbClearResult(res)
}
DBI::dbDisconnect(con)
}
# ALTER TABLE DROP COLUMN is not supported by sqlite
p.db.remove.column <- function(table="data", column.name) {
# con <- p.db.connection()
# if (column.name %in% DBI::dbListFields(con, table)) {
# column.name <- p.db.escape.name(column.name)
# q <- paste("ALTER TABLE", table, "DROP COLUMN", column.name, sep=" ")
# res <- DBI::dbSendQuery(con, q)
# DBI::dbClearResult(res)
# }
#
# DBI::dbDisconnect(con)
}
# p.db.extend.schema("kmeans_30_7", "integer", "Analytics", "Clusterings")
p.db.extend.schema <- function(name, type, group, group_type) {
con <- p.db.connection()
q <- paste("SELECT count(*) FROM schema WHERE name='", name, "'", sep="")
count <- unlist(DBI::dbGetQuery(con, q))
if (count == 0) {
values <- paste("'", c(name, type, group, group_type), "'", sep="", collapse=", ")
q <- paste("INSERT INTO schema (name, type, \"group\", group_type) VALUES(", values , ")", sep="")
res <- DBI::dbSendQuery(con, q)
DBI::dbClearResult(res)
}
DBI::dbDisconnect(con)
}
p.db.truncate.schema <- function(name) {
con <- p.db.connection()
q <- paste("SELECT count(*) FROM schema WHERE name='", name, "'", sep="")
count <- unlist(DBI::dbGetQuery(con, q))
if (count == 1) {
q <- paste("DELETE FROM schema WHERE name='", name, "'", sep="")
res <- DBI::dbSendQuery(con, q)
DBI::dbClearResult(res)
}
DBI::dbDisconnect(con)
}
# p.db.store(column.name="kmeans_30_7", 1:10, 8)
p.db.store <- function(column.name, rows = c(), value) {
column.name <- p.db.escape.name(column.name)
# NOTE: for now value is expected to be a numeric value.
con <- p.db.connection()
q <- paste("UPDATE data SET ", column.name, " = ", value, sep="")
if (length(rows) > 0) {
rows <- paste(as.character(rows), collapse=", ")
q <- paste(q, " WHERE row in (", rows, ")", sep="")
}
res <- DBI::dbSendQuery(con, q)
DBI::dbClearResult(res)
DBI::dbDisconnect(con)
}
p.db.storeList <- function(column.name, values) {
column.name <- p.db.escape.name(column.name)
#Note: list must have the row ids as the item names
#connect to DB
con <- p.db.connection()
#start TXN
dbBegin(con)
#build update statement for each item in the list,
# using the item name as a row id
print(paste("Query Build Start",Sys.time(),sep = " "))
queries<-paste("UPDATE data SET ", column.name, " = ", values, " WHERE row =", names(values),sep="")
#pass queries to DB
for(q in queries) {
DBI::dbSendQuery(con, q)
}
#commit changes
dbCommit(con)
DBI::dbDisconnect(con)
}
p.db.types <- function(variables) {
variables <- lapply(variables, p.db.escape.name)
# NOTE: for now value is expected to be a numeric value.
con <- p.db.connection()
q <- paste("SELECT name, type FROM schema WHERE name in ("
, paste(variables, collapse=", "), ")", sep="")
data <- DBI::dbGetQuery(con, q)
DBI::dbDisconnect(con)
data
}
# API exposed to the front-end
db.reset <- function() {
if (file.exists(p.db.file.name)) {
file.remove(p.db.file.name)
}
p.db.init()
}
# p.db.select(vars=c("M4", "M20"), rows=c(1,2,100,2300))
p.db.select <- function(table="data", vars=c(), rows=c()) {
vars <- lapply(vars, p.db.escape.name)
vars <- ifelse(length(vars) == 0,
"*",
paste(unlist(vars), collapse=", "))
q <- paste("SELECT ", vars, " FROM ", table, sep="")
if (length(rows) > 0) {
rows <- paste(as.character(rows), collapse=", ")
q <- paste(q, " WHERE row in (", rows, ")", sep="")
}
con <- p.db.connection()
data <- DBI::dbGetQuery(con, q)
DBI::dbDisconnect(con)
data
}
R.ICoVeR/dev/clean-opencpu-restart.sh deleted 100755 → 0
View file @ f9ef00c0
#!/bin/bash
sudo rm -rf /tmp/ocpu*
sudo rm -rf /tmp/opencpu*
sudo rm -rf /tmp/RParcoords
sudo service opencpu restart
sudo service opencpu-cache stop
R.ICoVeR/git-hooks/pre-commit deleted 100644 → 0
View file @ f9ef00c0
#!/bin/sh
# We're only interested in checking files that are in the js directory. The js
# files in inst/www/lib/* are considered to be external libraries over which we
# have no control or that fall outside the responsibility of this project.
files=$(git diff --cached --name-only --diff-filter=ACM | grep "^inst/www/js/.*.js$")
if [ "$files" = "" ]; then
exit 0
fi
pass=true
echo "\nValidating JavaScript:\n"
for file in ${files}; do
result=$(jslint --edition=2014-07-08 ${file} | grep "${file} is OK")
if [ "$result" != "" ]; then
echo "\t\033[32mJSLint Passed: ${file}\033[0m"
else
echo "\t\033[31mJSLint Failed: ${file}\033[0m"
pass=false
fi
done
echo "\nJavaScript validation complete\n"
if ! $pass; then
echo "\033[41mCOMMIT FAILED\033[0m"
echo "Your commit contains files that should pass JSLint but do not."
echo "Please fix the JSLint errors and try again.\n"
exit 1
else
echo "\033[42mCOMMIT SUCCEEDED\033[0m\n"
fi
R.ICoVeR/inst/www/app.min.js deleted 100644 → 0
View file @ f9ef00c0
This diff is collapsed.
R.ICoVeR/inst/www/calibrate.json deleted 100644 → 0
View file @ f9ef00c0
{
"title":"Test Data: columns only",
"x_axis_label": "Dim 1",
"y_axis_label": "Dim 2" ,
"dataExtents": [[-2.0,-2.0],[2.0,2.0]],
"dataItems":[
{"type":"column", "name":"CGGC.GCCG" , "x": 1.0, "y": -1.0},
{"type":"column", "name":"CGGC.GCCG" , "x": -1.0, "y": -1.0},
{"type":"column", "name":"CGGC.GCCG" , "x": -1.0, "y": 1.0},
{"type":"column", "name":"CGGC.GCCG" , "x": 1.0, "y": 1.0},
{"type":"column", "name":"CGGC.GCCG" , "x": 0.0, "y": 0.0},
{"type":"column", "name":"CGGC.GCCG" , "x": 0.5, "y": -0.5},
{"type":"column", "name":"CGGC.GCCG" , "x": -0.5, "y": -0.5},
{"type":"column", "name":"CGGC.GCCG" , "x": -0.5, "y": 0.5},
{"type":"column", "name":"CGGC.GCCG" , "x": 0.5, "y": 0.5}
]
}
R.ICoVeR/inst/www/css/dark.css deleted 100644 → 0
View file @ f9ef00c0
@import url("../libs/bootstrap/css/bootstrap-slate.min.css");
@import url("main.css");
.progress-bar-brushed {
background-color: #aeb9c2;
}
.parcoords .axis line, .parcoords .axis path {
fill: none;
stroke: #c8c8c8;
shape-rendering: crispEdges;
}
.parcoords text {
fill: #c8c8c8;
}
.dimredplot .individual.scatterplot .selected {
fill: white;
stroke: white;
}
.dimredplot .colormap .text {
fill: black;
}
\ No newline at end of file
R.ICoVeR/inst/www/css/light.css deleted 100644 → 0
View file @ f9ef00c0
@import url("../libs/bootstrap/css/bootstrap.min.css");
@import url("main.css");
.progress-bar-brushed {
background-color: #5ec6ff;
}
R.ICoVeR/inst/www/css/main.css deleted 100644 → 0
View file @ f9ef00c0
html, body {
height: calc(100% - 35px);
}
.form-control.ng-invalid {
border: 2px solid red;
}
.navbar {
margin-bottom: 0px;
}
.navbar .progress {
margin-bottom: 0px;
margin-right: 1em;
width: 150px;
}
.tab-content {
padding-top: 5px;
}
.adjusted-right-padding {
padding-right: 5px !important;
margin-right: 0 !important;
}
.adjusted-left-padding {
padding-left: 9px !important;
margin-left: 0 !important;
}
.no-left-padding {
padding-left: 0 !important;
margin-left: 0 !important;
}
.no-right-padding {
padding-right: 0 !important;
margin-right: 0 !important;
}
.form-group {
margin-bottom: 5px;
}
.modal-body select[multiple] {
min-height: 200px;
}
.modal-footer {
padding: 10px 15px;
}
.colorpatch {
display: block;
vertical-align: middle;
width: 37px;
height: 22px;
}
#SwitchOptions {
float: right;
}
#main {
height: 100%;
width: 100%;
margin: 50px auto 0px;
}
#top {
height: 60%;
margin-bottom: 10px;
}
#bottom {
height: 40%;
}
#options {
float: left;
position: absolute;
z-index: 3;
}
.parcoords {
background-color: transparent
}
#parcoords,
#colourmap,
#parcoords div,
#colourmap div {
height: 100%;
}
#charts {
height: 100%;
}
.tab-content {
height: calc(100% - 40px);
}
.tab-pane, .ng-isolate-scope, #dimRedPlots {
height: 100%;
}
#dimRedPlot {
height: 100%;
}
#twodmap {
height: 100%;
padding-left: 0px;
padding-right: 0px;
}
R.ICoVeR/inst/www/gulpfile.babel.js deleted 100644 → 0
View file @ f9ef00c0
import gulp from 'gulp';
import runSequence from 'run-sequence';
import gulpLoadPlugins from 'gulp-load-plugins';
const $ = gulpLoadPlugins();
gulp.task('scripts', () =>
gulp.src([
// Note: Since we are not using useref in the scripts build pipeline,
// you need to explicitly list your scripts here in the right order
// to be correctly concatenated
'libs/lodash/lodash-3.9.0.min.js',
'libs/jquery/jquery-1.11.1.min.js',
'libs/opencpu/opencpu-0.5.js',
'libs/d3/d3.min.js',
'libs/d3/d3.svg.multibrush.js',
'libs/d3/colorbrewer.js',
'libs/parcoords/d3.parcoords.js',
'libs/angularjs/angular-1.2.21.min.js',
'libs/ui-bootstrap/ui-bootstrap-tpls-0.12.1.min.js',
'libs/dimredplot/dimredplot.js',
'libs/dimredplot/scatterplot.js',
'libs/dimredplot/barplot.js',
'libs/dimredplot/variancepercentageplot.js',
'libs/dimredplot/colourmap.js',
'js/app.js',
'js/controllers/chartsctrl.js',
'js/controllers/clusterconfigctrl.js',
'js/controllers/clusterctrl.js',
'js/controllers/colorctrl.js',
'js/controllers/colourmapctrl.js',
'js/controllers/dataindicatorctrl.js',
'js/controllers/dimredctrl.js',
'js/controllers/dimreddisplayctrl.js',
'js/controllers/dimredplotctrl.js',
'js/controllers/escgctrl.js',
'js/controllers/exportctrl.js',
'js/controllers/filterctrl.js',
'js/controllers/manualcoloringctrl.js',
'js/controllers/namehighlightctrl.js',
'js/controllers/nameselectionctrl.js',
'js/controllers/parcoordsctrl.js',
'js/controllers/parcoordsvarsctrl.js',
'js/controllers/plotctrl.js',
'js/controllers/tagctrl.js',
'js/controllers/themectrl.js',
'js/controllers/variableselectionctrl.js',
'js/services/analytics.js',
'js/services/assert.js',
'js/services/color.js',
'js/services/dataset.js',
'js/services/dimredplot.js',
'js/services/opencpu.js',
'js/services/parcoords.js',
'js/services/r.js',
'js/services/tag.js'
])
.pipe($.concat('app.min.js'))
.pipe($.uglify({preserveComments: 'some', mangle: false}))
// Output files
.pipe(gulp.dest('.'))
.pipe($.size({title: 'scripts'}))
);
// Scan your HTML for assets & optimize them
gulp.task('html', () => {
const assets = $.useref.assets({searchPath: '{., ./css}'});
return gulp.src('index-raw.html')
.pipe($.rename('index.html'))
.pipe(assets)
// Remove any unused CSS
.pipe($.if('css/*.css', $.uncss({
html: ['index-raw.html']
})))
// Concatenate and minify styles
// In case you are still using useref build blocks
.pipe($.if('**/*.css', $.minifyCss()))
.pipe(assets.restore())
.pipe($.useref())
// Minify any HTML
.pipe($.if('*.html', $.minifyHtml()))
// Output files
.pipe(gulp.dest('.'))
.pipe($.size({title: 'html'}));
});
gulp.task('default', [], cb =>
runSequence(
['scripts', 'html'],
cb
)
);
R.ICoVeR/inst/www/index-raw.html deleted 100644 → 0
View file @ f9ef00c0
<!DOCTYPE html>
<html lang="en" ng-app="contigBinningApp">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title></title>
<link href="libs/fontawesome/css/font-awesome.css" rel="stylesheet">
<link href="libs/parcoords/d3.parcoords.css" rel="stylesheet">
<link href="libs/dimredplot/dimredplot.css" rel="stylesheet">
<link href="css/light.css" rel="stylesheet" id="maincss">
</head>
<body>
<nav class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container-fluid">
<div class="navbar-header">
<a class="navbar-brand">
<span style="color: #337ab7">ICoVeR</span> -
<span style="color: #337ab7">I</span>nteractive <span style="color: #337ab7">Co</span>ntig-bin
<span style="color: #337ab7">Ve</span>rification and <span style="color: #337ab7">R</span>efinement</a>
</div>
<form class="navbar-form navbar-right form-inline">
<div class="btn-group" ng-controller="ManualColoringCtrl" ng-show="manualColoringEnabled" dropdown>
<button type="button" class="btn btn-default" ng-disabled="!itemsBrushed" ng-style="{'background-color': colors[0]}">Apply color to selection</button>
<button type="button" class="btn btn-default dropdown-toggle" ng-disabled="!itemsBrushed" dropdown-toggle>
<span class="caret"></span>
<span class="sr-only">Toggle Dropdown</span>
</button>
<ul class="dropdown-menu brush-color" role="menu" id="brush-color-menu">
<li ng-repeat="color in colors">
<a href="#" ng-style="{'background-color': color}" ng-click="colorSelection(color)">
<span class="colorpatch"></span>
</a>
</li>
</ul>
</div>
<div class="form-group" ng-controller="NameHighlightCtrl" ng-hide="noHighlightAvailable">
<label class="control-label col-lg-4" for="rowNameHighlight">Highlight</label>
<input type="text" id="rowNameHighlight" class = "col-lg-5 input-sm" ng-model="rowName" ng-change="highlightRow()">
</div>
<div class="form-group" ng-controller="DataIndicatorCtrl">
<progress ng-click="changeScale()" max="1" animate="false">
<bar ng-repeat="bar in counts track by $index"
value="bar.rows / rowCount"
type="{{bar.type}}">
<b ng-hide="(bar.rows / rowCount) < 0.15">{{bar.rows}}</b>
</bar>
</progress>
</div>
<div class="form-group" ng-controller="ThemeCtrl">
<label class="control-label">Theme:</label>
<div class="btn-group">
<label class="btn btn-default" ng-model="theme" btn-radio="'light'">Light</label>
<label class="btn btn-default" ng-model="theme" btn-radio="'dark'">Dark</label>
</div>
</div>
</form>
</div>
</nav>
<div id="main" class="container-fluid">
<!-- Top half of the sceen -->
<div id="top" class="row">
<!--<div id="colourmap" class="col-lg-1">
<div class="colourmap" ng-controller="ColourmapCtrl">
</div>
</div>-->
<div id="parcoords" class="col-lg-12">
<div class="parcoords" ng-controller="ParcoordsCtrl">
</div>
</div>
</div>
<!-- Bottom half of the sceen -->
<div id="bottom" class="row" ng-controller="PlotCtrl">
<div id="options" ng-style="sliding">
<ng-include src="'js/templates/options.html'"></ng-include>
</div>
<div class="col-lg-1">
</div>
<!-- Scatterplot -->
<div id="charts" class="col-lg-11" ng-controller="ChartsCtrl">
<div class="row" id="dimRedPlots">
<div id="dimRedPlot" class="tab-pane container-fluid active" ng-class="dimredplotWidth" ng-repeat="analysis in analyses" ng-controller="DimRedPlotCtrl">
</div>
</div>
</div>
</div>
</div>
<!-- build:js(app) app.min.js -->
<script src="libs/lodash/lodash-3.9.0.min.js"></script>
<script src="libs/jquery/jquery-1.11.1.min.js"></script>
<script src="libs/opencpu/opencpu-0.5.js"></script>
<script src="libs/d3/d3.min.js"></script>
<script src="libs/d3/d3.svg.multibrush.js"></script>
<script src="libs/d3/colorbrewer.js"></script>
<script src="libs/parcoords/d3.parcoords.js"></script>
<script src="libs/dimredplot/dimredplot.js"></script>
<script src="libs/dimredplot/scatterplot.js"></script>
<script src="libs/dimredplot/barplot.js"></script>
<script src="libs/dimredplot/variancepercentageplot.js"></script>
<script src="libs/dimredplot/colourmap.js"></script>
<script src="libs/angularjs/angular-1.2.21.min.js"></script>
<script src="libs/ui-bootstrap/ui-bootstrap-tpls-0.12.1.min.js"></script>
<script src="js/app.js"></script>
<script src="js/services/dataset.js"></script>
<script src="js/controllers/namehighlightctrl.js"></script>
<script src="js/controllers/chartsctrl.js"></script>
<script src="js/controllers/clusterctrl.js"></script>
<script src="js/controllers/clusterconfigctrl.js"></script>
<script src="js/controllers/dataindicatorctrl.js"></script>
<script src="js/controllers/escgctrl.js"></script>
<script src="js/controllers/exportctrl.js"></script>
<script src="js/controllers/parcoordsctrl.js"></script>
<script src="js/controllers/parcoordsvarsctrl.js"></script>
<script src="js/controllers/filterctrl.js"></script>
<script src="js/controllers/dimredctrl.js"></script>
<script src="js/controllers/dimredplotctrl.js"></script>
<script src="js/controllers/colorctrl.js"></script>
<script src="js/controllers/manualcoloringctrl.js"></script>
<script src="js/controllers/themectrl.js"></script>
<script src="js/controllers/plotctrl.js"></script>
<script src="js/controllers/variableselectionctrl.js"></script>
<script src="js/controllers/dimreddisplayctrl.js"></script>
<script src="js/controllers/colourmapctrl.js"></script>
<script src="js/controllers/tagctrl.js"></script>
<script src="js/controllers/nameselectionctrl.js"></script>
<script src="js/services/analytics.js"></script>
<script src="js/services/assert.js"></script>
<script src="js/services/color.js"></script>
<script src="js/services/opencpu.js"></script>
<script src="js/services/parcoords.js"></script>
<script src="js/services/dimredplot.js"></script>
<script src="js/services/tag.js"></script>
<script src="js/services/r.js"></script>
<!-- endbuild -->
</body>
</html>
R.ICoVeR/inst/www/index.html deleted 100644 → 0
View file @ f9ef00c0
<!DOCTYPE html><html lang=en ng-app=contigBinningApp><head><meta charset=utf-8><meta http-equiv=X-UA-Compatible content="IE=edge"><meta name=viewport content="width=device-width, initial-scale=1"><title></title><link href=libs/fontawesome/css/font-awesome.css rel=stylesheet><link href=libs/parcoords/d3.parcoords.css rel=stylesheet><link href=libs/dimredplot/dimredplot.css rel=stylesheet><link href=css/light.css rel=stylesheet id=maincss></head><body><nav class="navbar navbar-default navbar-fixed-top" role=navigation><div class=container-fluid><div class=navbar-header><a class=navbar-brand><span style="color: #337ab7">ICoVeR</span> - <span style="color: #337ab7">I</span>nteractive <span style="color: #337ab7">Co</span>ntig-bin <span style="color: #337ab7">Ve</span>rification and <span style="color: #337ab7">R</span>efinement</a></div><form class="navbar-form navbar-right form-inline"><div class=btn-group ng-controller=ManualColoringCtrl ng-show=manualColoringEnabled><button type=button class="btn btn-default" ng-disabled=!itemsBrushed ng-style="{'background-color': colors[0]}">Apply color to selection</button><button type=button class="btn btn-default dropdown-toggle" ng-disabled=!itemsBrushed><span class=caret></span> <span class=sr-only>Toggle Dropdown</span></button><ul class="dropdown-menu brush-color" role=menu id=brush-color-menu><li ng-repeat="color in colors"><a href=# ng-style="{'background-color': color}" ng-click=colorSelection(color)><span class=colorpatch></span></a></li></ul></div><div class=form-group ng-controller=NameHighlightCtrl ng-hide=noHighlightAvailable><label class="control-label col-lg-4" for=rowNameHighlight>Highlight</label><input type=text id=rowNameHighlight class="col-lg-5 input-sm" ng-model=rowName ng-change=highlightRow()></div><div class=form-group ng-controller=DataIndicatorCtrl><progress ng-click=changeScale() max=1 animate=false><bar ng-repeat="bar in counts track by $index" value="bar.rows / rowCount" type={{bar.type}}><b ng-hide="(bar.rows / rowCount) < 0.15">{{bar.rows}}</b></bar></progress></div><div class=form-group ng-controller=ThemeCtrl><label class=control-label>Theme:</label><div class=btn-group><label class="btn btn-default" ng-model=theme btn-radio="'light'">Light</label><label class="btn btn-default" ng-model=theme btn-radio="'dark'">Dark</label></div></div></form></div></nav><div id=main class=container-fluid><div id=top class=row><div id=parcoords class=col-lg-12><div class=parcoords ng-controller=ParcoordsCtrl></div></div></div><div id=bottom class=row ng-controller=PlotCtrl><div id=options ng-style=sliding><ng-include src="'js/templates/options.html'"></ng-include></div><div class=col-lg-1></div><div id=charts class=col-lg-11 ng-controller=ChartsCtrl><div class=row id=dimRedPlots><div id=dimRedPlot class="tab-pane container-fluid active" ng-class=dimredplotWidth ng-repeat="analysis in analyses" ng-controller=DimRedPlotCtrl></div></div></div></div></div><script src=app.min.js></script></body></html>
\ No newline at end of file
R.ICoVeR/inst/www/js/app.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint indent: 2 */
/*global angular */
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
//ocpu.seturl("/ocpu/library/RParcoords/R");
// Create empty modules, which will be populated once the deps are loaded.
angular.module('contigBinningApp.controllers', ['ui.bootstrap']);
angular.module('contigBinningApp.services', []);
// Create a module for the application with the dependencies specified.
angular.module('contigBinningApp', [
'contigBinningApp.controllers',
'contigBinningApp.services'
]);
R.ICoVeR/inst/www/js/controllers/chartsctrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint browser: true, todo:true, nomen: true, indent: 2 */
/*global angular, crpgl, d3, ocpu, _, $*/
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('ChartsCtrl', function ($scope) {
'use strict';
$scope.location = false;
/*jslint unparam: true */
$scope.$on('DataSet::schemaLoaded', function (e, schema) {
// FIXME: we make a lot of assumptions in this function. For now this is
// just a quick hack to make things work (tm) for some initial
// testing with datasets that have spatial information.
// For this widget to work, the schema must have a group with the type
// Location.*, which must in turn have an x and y variable.
function selector(v) {
return v.group_type === 'Location.Dense' || v.group_type === 'Location.Sparse';
}
var location = _.groupBy(_.select(schema, selector), 'group');
// For now we only support one location, so let's get the first one.
if (_.keys(location).length > 0) {
$scope.location = _.groupBy(location[_.first(_.keys(location))], 'name');
}
});
/*jslint unparam: false */
});
R.ICoVeR/inst/www/js/controllers/clusterconfigctrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint indent: 2 */
/*global angular */
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('ClusterConfigCtrl', function ($scope, $modalInstance, options, DataSet) {
'use strict';
// It is possible that there are less than 30 individuals, in which case we can not use 30 clusters.
// The default number of clusters in this case is less than the number of rows as it would otherwise,
// make no sense.
var previousCentersCount = Math.min(30, Math.floor(Math.sqrt(DataSet.data().length)));
function updateControllerState() {
$scope.specified.identifier = $scope.specified.method.name
+ ($scope.specified.centers !== -1 ? '_' + $scope.specified.centers : "")
+ '_' + ($scope.specified.variables.length || 0);
$scope.configurationInvalid =
($scope.specified.centers < 2 && $scope.specified.centers !== -1)
|| $scope.specified.variables.length < 1;
}
$scope.options = options;
$scope.configurationInvalid = true;
$scope.specified = {
method: $scope.options.methods[0],
identifier: $scope.options.methods[0].name + '_' + previousCentersCount + '_0',
centers: previousCentersCount, // NOTE: The naming is kmeans specific
variables: []
};
$scope.$watch('specified.centers', updateControllerState);
$scope.$watch('specified.variables', updateControllerState);
$scope.$watch('specified.method', updateControllerState);
$scope.ok = function () {
$modalInstance.close($scope.specified);
};
$scope.hideCenters = function () {
if ($scope.specified.method.name !== "kmeans") {
previousCentersCount = $scope.specified.centers;
$scope.specified.centers = -1;
return true;
}
if ($scope.specified.centers === -1) {
$scope.specified.centers = previousCentersCount;
}
return false;
};
$scope.cancel = function () {
$modalInstance.dismiss();
};
});
R.ICoVeR/inst/www/js/controllers/clusterctrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint indent: 2, nomen: true */
/*global angular, _ */
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('ClusterCtrl', function ($scope, $modal, Analytics, R) {
'use strict';
var d = {
schema: undefined
};
function setVariables() {
$scope.options.variables = _.filter(d.schema, function (variable) {
return R.is.numeric(variable.type) && variable.analysable;
});
}
function performClustering(config) {
var args = {};
// FIXME: Generalize this code, we don't want to change this code for
// every clustering method we add.
if (config.method.name === "kmeans") {
args.centers = config.centers;
} else if (config.method.name !== "correlation") {
//FIXME get rid of this hard coded value, change it to a simple else
throw "Unknown clustering method: " + config.method.name;
}
Analytics.cluster(
config.method.name,
_.map(config.variables,
function (variable) { return variable.name; }),
args,
config.identifier
);
}
// Available clustering options.
$scope.options = {
methods: [],
variables: [],
valid: function () {
return $scope.options.methods.length > 0
&& $scope.options.variables.length > 2;
}
};
$scope.canCluster = false;
/*jslint unparam: true */
$scope.$on('DataSet::schemaLoaded', function (e, schema) {
d.schema = schema;
setVariables();
$scope.canCluster = $scope.options.valid();
});
/*jslint unparam: false */
/*jslint unparam: true */
$scope.$on('Analytics::clusterMethodsAvailable', function (e, methods) {
$scope.options.methods = methods;
$scope.canCluster = $scope.options.valid();
});
/*jslint unparam: false */
$scope.openSelectionDialog = function () {
var dialog = $modal.open({
templateUrl: 'js/templates/clusterconfig.html',
size: 'md',
controller: 'ClusterConfigCtrl',
resolve: {
options: function () {
return $scope.options;
}
}
});
dialog.result.then(performClustering);
};
});
R.ICoVeR/inst/www/js/controllers/colorctrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint indent: 2, nomen: true */
/*global angular, _*/
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('ColorCtrl', function ($scope, R, Color) {
'use strict';
var d = {
methods: undefined,
initialSchemaLoad: true
};
function onMethodChange() {
if (d.methods === undefined) {
$scope.colorSchemes = [];
$scope.colorScheme = undefined;
return;
}
$scope.colorSchemes = d.methods[$scope.colorMethod];
if ($scope.colorSchemes === undefined) {
$scope.colorSchemes = [];
} else if (!_.isArray($scope.colorSchemes)) {
$scope.colorSchemes = [$scope.colorSchemes];
}
if ($scope.colorScheme === undefined
|| !_.contains($scope.colorSchemes, $scope.colorScheme)) {
$scope.colorScheme = $scope.colorSchemes[0];
}
}
function onVariableChange() {
if ($scope.colorVariable && R.is.numeric($scope.colorVariable.type)) {
d.methods = Color.configuration().numeric;
} else if ($scope.colorVariable && R.is.factor($scope.colorVariable.type)) {
d.methods = Color.configuration().factor;
} else {
d.methods = undefined;
$scope.colorMethod = undefined;
}
$scope.colorMethods = _.keys(d.methods);
if ($scope.colorMethod === undefined
|| !_.contains($scope.colorMethods, $scope.colorMethod)) {
$scope.colorMethod = $scope.colorMethods[0];
} else {
onMethodChange();
}
}
function onOpacityChange() {
Color.opacity($scope.opacity);
}
$scope.variables = [];
$scope.colorMethods = [];
$scope.colorSchemes = [];
$scope.colorVariable = undefined;
$scope.colorMethod = undefined;
$scope.colorScheme = undefined;
$scope.opacity = 0.05;
$scope.applyColoring = function () {
if ($scope.colorVariable !== undefined) {
Color.color($scope.colorVariable.name, $scope.colorMethod, $scope.colorScheme);
}
};
function updateVariables(schema) {
$scope.dataAvailable = true;
$scope.variables = _.filter(schema, function (variable) {
return R.is.numeric(variable.type) || R.is.factor(variable.type);
});
// Make sure that the manual selection option is on top
var manualIndex = _.findIndex($scope.variables, "name", "Manual selection"),
manualSelectionVar,
colorVariable;
if (manualIndex !== -1) {
manualSelectionVar = $scope.variables[manualIndex];
$scope.variables.splice(manualIndex, 1);
$scope.variables.splice(0, 0, manualSelectionVar);
}
if ($scope.colorVariable !== undefined) {
colorVariable = _.find($scope.variables, "name", $scope.colorVariable.name);
$scope.colorVariable = colorVariable;
}
}
$scope.$on('Colors::changed', function () {
$scope.colorVariable = _.find($scope.variables, "name", Color.colorVariable());
$scope.colorMethod = Color.colorMethod();
$scope.colorScheme = Color.colorSchemeName();
});
$scope.$on('DataSet::schemaLoaded', function (e, schema) {
/*jslint unparam: true */
updateVariables(schema);
if (d.initialSchemaLoad) {
// We only want to change the color scheme implicitly the first time we
// recieve data. Afterwards it's up to the user to change the color
// scheme to his or her likening.
d.initialSchemaLoad = false;
$scope.colorVariable = _.find(schema, { 'name': 'GC_CONTENT' });
$scope.colorMethod = "Decile";
$scope.colorScheme = "yellow_to_red";
$scope.applyColoring();
$scope.$watch('colorVariable', onVariableChange);
$scope.$watch('colorMethod', onMethodChange);
$scope.$watch('opacity', onOpacityChange);
}
});
});
R.ICoVeR/inst/www/js/controllers/colourmapctrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint browser:true, unparam: true, indent: 2, nomen: true */
/*global angular, d3, $, _, list*/
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('ColourmapCtrl', function ($scope, $window, $element, DataSet, ParCoords, Color) {
'use strict';
//$scope.renderColourmap = false;
d3.select($element[0]).style("display", "none");
/// private Controller vars
var d = {
colourMap: list.ColourMap(),
colourMapScale: d3.scale.linear(),
colourMapGroup: null,
title: null
};
/// private controller functions
function render() {
d.colourMapGroup
.select("g")
.call(d.colourMap);
}
function resize() {
d.colourMapScale.range([$element[0].clientHeight - 15, 22]);
d.colourMap
.scale(d.colourMapScale);
d.colourMapGroup.attr("height", $element[0].clientHeight);
d.title
.attr("y", d.title.node().clientHeight)
.attr("x", -d.title.node().clientWidth + 20);
render();
}
/// Initialization
d.colourMapScale
.domain([0, 1])
.range([$element[0].clientHeight, 0]);
d.colourMap
.width(20)
.axisSide("left")
.extent([0, 0])
.scale(d.colourMapScale);
/*.on("brush", function () {
});*/
d.colourMapGroup = d3.select($element[0]).selectAll("svg.colourmap").data([true]);
d.colourMapGroup.enter()
.append("svg")
.attr("class", "colourmap")
.append("g")
.attr("transform", "translate(" + 60 + ", 4)")
.append("text")
.attr("class", "label");
d.title = d.colourMapGroup.select("text.label")
.text("influence");
angular.element($window).bind('resize', resize);
$(document).ready(resize);
/// Scope extensions
$scope.$on("Colors::changed", function (e, rowColors) {
/*jslint unparam:true todo:true*/
//$scope.renderColourmap = true;
//TODO fix this so it actualles uses ng-show
d3.select($element[0]).style("display", "block");
//d.colourMapScale.domain(domain);
d.colourMap.scale(d.colourMapScale);
d.colourMap.colourFunction(Color.colorFn());
d.title.text(Color.colorVariable());
resize();
});
});
R.ICoVeR/inst/www/js/controllers/dataindicatorctrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint indent: 2 */
/*global angular */
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('DataIndicatorCtrl', function ($scope) {
'use strict';
var overallRowCount = 0, // The total number of rows in the dataset
currentRowCount = 0, // The current number of rows in the views
brushedRowCount = 0; // The current number of rows which are brushed
$scope.rowCount = 0;
$scope.counts = [];
/*jslint unparam: true */
$scope.$on("DataSet::brushed", function (ev, rows) {
brushedRowCount = rows.length;
if (rows.length > 0) {
$scope.counts = [
{ rows: brushedRowCount, type: "brushed" },
{ rows: currentRowCount - brushedRowCount, type: "" }
];
} else {
$scope.counts = [{ rows: currentRowCount, type: "" }];
}
});
/*jslint unparam: false */
/*jslint unparam: true */
$scope.$on("DataSet::filtered", function (ev, rows) {
currentRowCount = rows.length;
brushedRowCount = 0;
if ($scope.rowCount === overallRowCount) {
$scope.counts = [{ rows: currentRowCount, type: "" }];
} else {
$scope.rowCount = currentRowCount;
$scope.counts = [{ rows: currentRowCount, type: "" }];
}
});
/*jslint unparam: false */
$scope.changeScale = function () {
if ($scope.rowCount === overallRowCount) {
$scope.rowCount = currentRowCount;
} else {
$scope.rowCount = overallRowCount;
}
};
/*jslint unparam: true */
$scope.$on("App::configurationLoaded", function (ev, cfg) {
overallRowCount = currentRowCount = cfg.data.dimensions.rows;
brushedRowCount = 0;
$scope.rowCount = currentRowCount;
$scope.counts = [{ rows: currentRowCount, type: "" }];
});
/*jslint unparam: false */
});
R.ICoVeR/inst/www/js/controllers/dimredctrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint indent: 2, nomen: true */
/*global angular, _, list */
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('DimRedCtrl', function ($scope, $modal, Analytics, R, DimRedPlot, DataSet) {
'use strict';
var d = {
schema: undefined
};
function createGroupTypeRestrictionTest(restriction) {
var groupType = restriction,
test = function (gt) { return gt === groupType; };
if (restriction[0] === '!') {
groupType = restriction.substr(1);
test = function (gt) { return gt !== groupType; };
}
return function (variable) {
return test(variable.group_type);
};
}
function createTypeRestrictionTest(restriction) {
if (restriction === 'schema.numeric') {
return function (variable) {
return R.is.numeric(variable.type);
};
}
if (restriction === 'schema.factor') {
return function (variable) {
return R.is.factor(variable.type);
};
}
throw ('Unsupported type restriction');
}
function updateSelectedVariables(variables) {
if (variables.length === 0) {
$scope.selectionText = "Select variables...";
$scope.selectionTextLong = "No variables selected";
} else {
var text = _.reduce(variables, function (str, variable) {
return str === "" ? variable.name : str + ", " + variable.name;
}, "");
if (text.length > "Select variables...".length) {
$scope.selectionTextLong = text;
text = "Selected " + variables.length + " variables";
}
$scope.selectionText = text;
$scope.selectedVariables = variables;
}
$scope.configurationInvalid = $scope.selectedVariables.length === 0;
}
function setVariables() {
if ($scope.selectedDimRedMethod === undefined || d.schema === undefined) {
$scope.variables = [];
} else {
// FIXME: This is a sloppy implementation as I didn't think this out
// very well. Actually, it should allow for multiple types for
// group restriction.
var restrictions = $scope.selectedDimRedMethod.restrict,
matchesGroupRestriction = createGroupTypeRestrictionTest(restrictions.group_type),
matchesTypeRestriction = createTypeRestrictionTest(restrictions.type);
$scope.variables = _.filter(d.schema, matchesGroupRestriction);
$scope.variables = _.filter($scope.variables, matchesTypeRestriction);
$scope.variables = _.filter($scope.variables, function (variable) {
return variable.analysable;
});
}
}
$scope.selectionText = "Select variables...";
$scope.selectionTextLong = "No variables selected";
$scope.variables = [];
$scope.dimRedMethods = [];
$scope.configurationInvalid = true;
$scope.selectedDimRedMethod = $scope.dimRedMethods[0];
$scope.selectedVariables = [];
$scope.$watch('selectedDimRedMethod', function (newMethod) {
if (newMethod === undefined) { return; }
setVariables();
});
$scope.$on('DimRedPlot::variablesSelected', function (e, dimRedMethod) {
/*jslint unparam: true*/
$scope.dimRedMethods.some(function (method) {
if (method.name === dimRedMethod) {
$scope.selectedDimRedMethod = method;
return true;
}
return false;
});
setVariables();
var variables = [],
selectedVariables = DimRedPlot.selectedVariables();
_.forEach(selectedVariables, function (variable) {
$scope.variables.some(function (schemaVariable) {
if (schemaVariable.name === variable) {
variables.push(schemaVariable);
return true;
}
return false;
});
});
updateSelectedVariables(variables);
});
function updateCaOnTnf() {
$scope.selectedVariables = _.filter($scope.variables, function (variable) {
return variable.group === "Tetra nucleotide frequencies";
});
updateSelectedVariables($scope.selectedVariables);
if ($scope.selectedVariables.length > 2) {
$scope.reduceDimensionality();
}
}
/*jslint unparam: true */
$scope.$on('DataSet::schemaLoaded', function (e, schema) {
$scope.dataAvailable = true;
d.schema = schema;
setVariables();
});
/*jslint unparam: false */
$scope.$on('DataSet::filtered', updateCaOnTnf);
/*jslint unparam: true */
$scope.$on('Analytics::dimRedMethodsAvailable', function (e, methods) {
// ICoVeR: For now we only suppor CA on (T|P)NF, so we filter out all
// other dim. red. methods.
$scope.dimRedMethods = _.filter(methods, function (m) { return m.name === "ca"; });
$scope.selectedDimRedMethod = $scope.dimRedMethods[0];
setVariables();
});
/*jslint unparam: false */
$scope.$on('Analytics::dimensionalityReduced', function () {
$scope.configurationInvalid =
$scope.selectedVariables.length === 0
|| $scope.selectedDimRedMethod === undefined;
});
$scope.openSelectionDialog = function () {
var dialog = $modal.open({
templateUrl: 'js/templates/selectvars.html',
size: 'sm',
controller: 'VariableSelectionCtrl',
resolve: {
variables: function () {
return $scope.variables;
},
selected: function () {
return $scope.selectedVariables;
}
}
});
dialog.result.then(updateSelectedVariables);
};
$scope.reduceDimensionality = function () {
var drMethod = $scope.selectedDimRedMethod.name,
vars = _.pluck($scope.selectedVariables, 'name');
// For quick loading purposes we are making sure here that all variables requested are loaded
DataSet.get(vars, function () { return; });
$scope.configurationInvalid = true;
Analytics.reduce(drMethod, vars);
};
});
R.ICoVeR/inst/www/js/controllers/dimreddisplayctrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint indent: 2, todo:true, nomen:true */
/*global angular, d3, _ */
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('DimRedDisplayCtrl', function ($scope, $rootScope) {
'use strict';
$scope.clusters = [];
$scope.cluster = undefined;
function updateState(dimRedData) {
// NOTE: The backend calculates up to 12 clustering levels (at most).
var maxClusterCount = Math.min(dimRedData.projections.length, 13);
$scope.clusters = _.map(_.range(2, maxClusterCount),
function (val) {
return { count: val, label: String(val) };
});
$scope.clusters.unshift({ count: 0, label: "No clustering" });
$scope.cluster = $scope.clusters[0];
}
/*jslint unparam: true */
$scope.$on("Analytics::dimensionalityReduced", function (ev, method, session) {
session.getObject(updateState);
});
/*jslint unparam: false */
$scope.$watch('cluster', function (newCount) {
if (newCount !== undefined) {
$rootScope.$broadcast("DimRedDisplay::cluster", newCount.count);
}
});
});
R.ICoVeR/inst/www/js/controllers/dimredplotctrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint browser: true, todo:true, nomen: true, indent: 2 */
/*global angular, crpgl, list, d3, ocpu, _, $*/
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('DimRedPlotCtrl', function ($scope, $element, $window, DimRedPlot, DataSet, Color) {
'use strict';
var dimredplot = list.DimRedPlot();
function changeSelection() {
d3.select($element[0]).selectAll("div.dimredplot").call(dimredplot);
}
function resize() {
var div = d3.select($element[0]).selectAll("div.dimredplot").data([$scope.analysis]);
div.enter()
.append("div")
.attr("class", "dimredplot")
.style("height", "100%")
.style("width", "100%");
dimredplot
.width(div.node().clientWidth)
.height(div.node().clientHeight);
}
$scope.$on("DimRedPlot::resize", function (e, numOfPlots) {
/*jslint unparam:true*/
dimredplot.automaticResize(numOfPlots === 1);
dimredplot.invertPlotOrder(numOfPlots === 2 && $scope.analysis.plotIdx === 0);
resize();
changeSelection();
});
angular.element($window).bind('resize', resize);
$(document).ready(resize);
$scope.$on("DimRedPlot::selectionUpdated", function (ev, method) {
/*jslint unparam:true*/
if (method !== $scope.analysis.method[0]) {
dimredplot.individualSelections(DimRedPlot.selections.individual);
}
dimredplot.variableInfluences(DimRedPlot.influences.variable);
changeSelection();
});
$scope.$on("DimRedPlot::variablesSelected", function (ev, method) {
/*jslint unparam:true*/
if (method !== $scope.analysis.method[0]) {
dimredplot.variableSelections(DimRedPlot.selections.variable);
}
dimredplot.individualInfluences(DimRedPlot.influences.individual);
changeSelection();
});
function setColor() {
/*jslint todo:true*/
var variable = Color.colorVariable(),
schema;
if (variable !== undefined) {
schema = _.find(DataSet.schema(), "name", variable);
}
// TODO: Currently there is no support for colour mapping categorical variables,
// so for now we will just ignore these. In the future we may just want to upgrade
// the colourmap chart or not show a colour map, just colour the points.
if (schema === undefined) {
return;
}
DataSet.get([variable], function (rows) {
var variableValues = {};
_.each(rows, function (row) {
variableValues[row.row] = row[variable];
});
dimredplot
.colorFunction(Color.colorFn())
.colorVariableName(variable)
.colorVariableValues(variableValues);
});
}
function updatePlot() {
$scope.analysis.flags = {pointsChanged: true};
function calculateContribution(axesIdx) {
if ($scope.analysis.individualProjections === undefined) {
return;
}
var xyContributions = {},
xVariance = $scope.analysis.explainedVariance[axesIdx[0]],
yVariance = $scope.analysis.explainedVariance[axesIdx[1]];
_.forEach($scope.analysis.individualProjections, function (projection) {
xyContributions[projection.id] = (projection.contrib[axesIdx[0]] * xVariance +
projection.contrib[axesIdx[1]] * yVariance) /
(xVariance + yVariance);
});
DataSet.addVariable($scope.analysis.method[0].toUpperCase() + " x+y contribution", xyContributions, "numeric", "Analytics");
}
dimredplot
.originSize(30)
.originVisible(true)
.on("changeVariableSelection", function (drp) {
$scope.$apply(function () {
DimRedPlot.changeVariableSelection($scope.analysis.method[0], drp.variableSelections());
});
})
.on("changeIndividualSelection", function (drp) {
$scope.$apply(function () {
DimRedPlot.changeIndividualSelection($scope.analysis.method[0], drp.individualSelections());
});
})
.on("changeAxes", function (drp, axesIdx) {
/*jslint unparam:true*/
calculateContribution(axesIdx);
})
.individualSelections(DimRedPlot.selections.individual)
.variableSelections(DimRedPlot.selections.variable)
.individualInfluences(DimRedPlot.influences.individual)
.variableInfluences(DimRedPlot.influences.variable);
resize();
calculateContribution([0, 1]);
setColor();
changeSelection();
}
$scope.$on("Colors::changed", function () {
setColor();
changeSelection();
});
updatePlot();
});
R.ICoVeR/inst/www/js/controllers/escgctrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint indent: 2, nomen: true */
/*global angular, _*/
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('ESCGCtrl', function ($rootScope, $scope, DataSet) {
'use strict';
var d = {};
$scope.uniqueGenes = 0;
$scope.multiCopyGenes = '0 / 0';
$scope.missingGenes = 0;
$scope.totalGenes = 0;
function updateGeneCounts(data) {
var contigs = d.contigs,
escg = {},
multiCopyGenes = 0,
additionalCopies = 0;
_.forEach(data, function (datum) {
var contig = datum.CONTIG,
asseccesions;
if (contigs.hasOwnProperty(contig)) {
asseccesions = _.isArray(contigs[contig]) ? contigs[contig] : [contigs[contig]];
_.forEach(asseccesions, function (a) {
escg[a] = escg[a] === undefined ? 1 : escg[a] + 1;
});
}
});
_.forEach(Object.getOwnPropertyNames(escg), function (asseccion) {
if (escg[asseccion] > 1) {
multiCopyGenes = multiCopyGenes + 1;
additionalCopies = additionalCopies + escg[asseccion] - 1;
}
});
$scope.uniqueGenes = Object.getOwnPropertyNames(escg).length;
$scope.multiCopyGenes = multiCopyGenes + ' / ' + additionalCopies;
$scope.missingGenes = d.asseccesions.length - $scope.uniqueGenes;
$scope.totalGenes = $scope.uniqueGenes + additionalCopies;
}
/*jslint unparam: true */
$rootScope.$on('App::configurationLoaded', function (e, cfg) {
d.asseccesions = cfg.escg.asseccion;
d.contigs = cfg.escg.contigs;
DataSet.get('CONTIG', updateGeneCounts);
});
$rootScope.$on('DataSet::brushed', function (e, data) {
if (data.length > 0) {
updateGeneCounts(data);
} else {
updateGeneCounts(DataSet.data());
}
});
$rootScope.$on('DataSet::filtered', function (e, data) {
updateGeneCounts(data);
});
/*jslint unparam: false */
});
R.ICoVeR/inst/www/js/controllers/exportctrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint indent: 2, nomen: true */
/*global angular, _*/
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('ExportCtrl', function ($rootScope, $scope, DataSet) {
'use strict';
var d = {
all: [],
rows: []
};
$scope.url = undefined;
$scope.idStrings = "";
$scope.exportMethods = ["all"];
$scope.exportMethod = $scope.exportMethods[0];
/*jslint unparam: true */
$rootScope.$on("DataSet::brushed", function (ev, rows) {
d.rows = rows;
// Reset the url on brush change to avoid confusion of what is being
// exported when clicking the url.
$scope.url = undefined;
if (rows.length > 0) {
$scope.exportMethods = ["all", "brushed"];
$scope.exportMethod = $scope.exportMethods[1];
} else {
$scope.exportMethods = ["all"];
$scope.exportMethod = $scope.exportMethods[0];
}
});
/*jslint unparam: false */
/*jslint unparam: true */
$scope.$on('DataSet::schemaLoaded', function (e, schema) {
DataSet.get(["CONTIG"], function (data) {
d.all = data;
});
});
/*jslint unparam: false */
$scope.export = function () {
var data = d.rows.length > 0 ? d.rows : d.all,
rows = _.map(data, function (row) { return row.CONTIG; });
$scope.idStrings = _.reduce(rows, function (str, id) {
return str + (str.length > 0 ? "\n" : "") + id;
}, "");
};
});
R.ICoVeR/inst/www/js/controllers/filterctrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint indent: 2 */
/*global angular */
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('FilterCtrl', function ($scope, DataSet) {
'use strict';
$scope.itemsBrushed = false;
$scope.dataFiltered = false;
$scope.filteringInProgress = false;
$scope.keepSelected = function () {
$scope.filteringInProgress = true;
DataSet.filter(DataSet.FilterMethod.KEEP);
};
$scope.removeSelected = function () {
$scope.filteringInProgress = true;
DataSet.filter(DataSet.FilterMethod.REMOVE);
};
$scope.reloadData = function () {
DataSet.filter(DataSet.FilterMethod.RESET);
};
$scope.$on('DataSet::loaded', function () { $scope.dataFiltered = false; });
$scope.$on('DataSet::filtered', function () {
$scope.filteringInProgress = false;
$scope.dataFiltered = DataSet.filtered();
});
/*jslint unparam: true */
$scope.$on('DataSet::brushed', function (e, rows) {
$scope.itemsBrushed = rows.length > 0;
});
/*jslint unparam: false */
});
R.ICoVeR/inst/www/js/controllers/manualcoloringctrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint indent: 2, nomen: true */
/*global angular, _*/
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('ManualColoringCtrl', function ($scope, Color) {
'use strict';
$scope.colors = [];
$scope.manualColoringEnabled = false;
$scope.itemsBrushed = false;
$scope.$on("Colors::changed", function () {
if (Color.colorVariable() === "Manual selection") {
if (!$scope.manualColoringEnabled || $scope.colors !== Color.colorScheme()) { // Manual selection is already on
$scope.manualColoringEnabled = true;
$scope.colors = Color.colorScheme();
}
} else {
$scope.manualColoringEnabled = false;
}
});
$scope.colorSelection = function (color) {
Color.colorBrushed(color);
};
$scope.$on("DataSet::brushed", function (e, rows) {
/*jslint unparam:true*/
$scope.itemsBrushed = rows.length > 0;
});
});
R.ICoVeR/inst/www/js/controllers/namehighlightctrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint indent: 2 */
/*global angular */
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('NameHighlightCtrl', function ($scope, DataSet, ParCoords) {
'use strict';
var nameHash = {},
variables = [];
function buildNameHash(data) {
nameHash = {};
data.forEach(function (d, dataIndex) {
variables.forEach(function (v) {
nameHash[d[v]] = dataIndex;
});
});
$scope.noHighlightAvailable = false;
// if a row is highlighted before the event that caused the rebuild
// we still want it to be highlighted after
$scope.highlightRow();
}
/*jslint unparam: true */
$scope.$on('DataSet::schemaLoaded', function (e, schema) {
variables = [];
schema.forEach(function (d) {
if (d.group === "Id") {
variables.push(d.name);
}
});
if (variables.length > 0) {
DataSet.get(variables, buildNameHash);
}
});
/*jslint unparam: false */
/*jslint unparam: true */
$scope.$on('DataSet::filtered', function (e, filteredData) {
// remove highlight... it will be reapplied once the filter returns
ParCoords.highlightRow(-1);
if (variables.length > 0) {
buildNameHash(filteredData);
}
});
/*jslint unparam: false */
$scope.noHighlightAvailable = true;
$scope.highlightRow = function () {
// called by ng_change directive on the rowName input in the UI
var highlightIndex = -1;
if (nameHash.hasOwnProperty($scope.rowName)) {
highlightIndex = nameHash[$scope.rowName];
}
ParCoords.highlightRow(highlightIndex);
};
});
R.ICoVeR/inst/www/js/controllers/nameselectionctrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint indent: 2 */
/*global angular */
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('NameSelectionCtrl', function ($scope, $modalInstance, selectedName) {
'use strict';
// https://stackoverflow.com
// /questions/21379173/angularjs-ui-modal-and-select-doesnt-update-the-scope-values
$scope.data = {
selectedName: "",
placeholderName: selectedName
};
$scope.ok = function () {
if ($scope.data.selectedName === "") {
$scope.data.selectedName = $scope.data.placeholderName;
}
$modalInstance.close($scope.data.selectedName);
};
$scope.cancel = function () {
$modalInstance.dismiss();
};
});
R.ICoVeR/inst/www/js/controllers/parcoordsctrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint browser:true, unparam: true, indent: 2, nomen: true */
/*global angular, d3, $, _*/
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('ParcoordsCtrl', function ($scope, $window, $element, DataSet, ParCoords) {
'use strict';
/// private Controller vars
var d = {
parcoords: d3.parcoords()($element[0]),
currentHighlightRow: -1,
orderedVariables: []
};
/// private controller functions
function render() {
if ($scope.brushed === undefined || $scope.brushed.length !== 0) {
$scope.brushed = [];
DataSet.brush($scope.brushed, "parcoords");
}
d.parcoords
.brushReset()
.autoscale()
.updateAxes()
.render();
}
function resize() {
d.parcoords
.width($element[0].clientWidth)
.height($element[0].clientHeight)
.resize();
render();
}
/*
function transformBrushExtents() {
var brushData = {extents: {}, categories: {}},
b = null,
getDomain = function (item, index) {
if (item >= d.parcoords.brushExtents()[b][0] && item <= d.parcoords.brushExtents()[b][1]) {
brushData.categories[b].push(d.parcoords.yscale[b].domain()[index]);
}
};
for (b in d.parcoords.brushExtents()) {
if (d.parcoords.brushExtents().hasOwnProperty(b)) {
if (d.parcoords.types()[b] === "string") {
brushData.categories[b] = [];
d.parcoords.yscale[b].range().forEach(getDomain);
} else {
brushData.extents[b] = d.parcoords.brushExtents()[b];
}
}
}
return brushData;
}
*/
function setDimensions() {
var dims = _.pluck(ParCoords.selectedVariables, "name"),
types = {},
averages = {},
brushedData = d.parcoords.brushed(),
dimensionsChanged;
d.orderedVariables = _.filter(d.orderedVariables, function (variable) {
return _.contains(dims, variable);
});
_.each(dims, function (variable) {
if (!_.contains(d.orderedVariables, variable)) {
d.orderedVariables.push(variable);
}
});
_.each(ParCoords.selectedVariables, function (dim) {
if (dim.type === "factor") {
types[dim.name] = "string";
} else {
types[dim.name] = "number";
}
});
// We need to make sure that the scales for the dimensions we want are calculated,
// since we need those scales in the next block of code.
dimensionsChanged = d.orderedVariables.length !== d.parcoords.dimensions().length || d.orderedVariables.some(function (dimension) {
return d.parcoords.dimensions().indexOf(dimension) === -1;
});
d.parcoords.dimensions(d.orderedVariables);
if (dimensionsChanged) {
d.parcoords
.types(types)
.autoscale()
.updateAxes();
}
if (ParCoords.variableSorting !== "none") {
if (brushedData === false) {
brushedData = d.parcoords.data();
}
_.each(d.orderedVariables, function (variable) {
var catCounts = {},
maxCategory,
maxCount = 0;
if (types[variable] === "string") {
_.each(brushedData, function (row) {
var category = row[variable];
if (catCounts[category] === undefined) {
catCounts[category] = 1;
} else {
catCounts[category] += 1;
}
if (catCounts[category] > maxCount) {
maxCategory = category;
}
});
averages[variable] = maxCategory;
} else {
averages[variable] = _.sum(brushedData, variable) / brushedData.length;
}
});
d.parcoords.reorder(averages);
}
}
/// Initialization
d.parcoords
.mode("queue")
.brushedColor("black")
.alphaOnBrushed(0.5)
.rate(250)
.alpha(0.05)
.render()
.createAxes()
.brushMode("1D-axes-multi")
.reorderable()
.dimensionTitleRotation(-25)
.on("brushend", function () {
// NOTE: the brushend event from parcoords is "outside" angular, so we
// have to wrap it in $scope.$apply to make sure that other
// controllers are updated appropriately.
$scope.$apply(function () {
var brushed = d.parcoords.brushed();
// d3.parcoords.js returns the full data set when no brush is set.
// This can't be changed in the component for legacy reasons. However,
// when no brushes are set, no data is brushed, so let's work around
// this issue here.
brushed = brushed.length === d.parcoords.data().length ? [] : brushed;
DataSet.brush(brushed, "parcoords");
if (ParCoords.variableSorting !== "none") {
setDimensions();
d.parcoords.render();
}
});
})
.on("axesreorder", function (variables) {
d.orderedVariables = variables;
});
function updateSharedAxes() {
var dims = _.pluck(ParCoords.sharedScaleVariables, "name"),
domain;
// First we determine the min/max required extents of the domain
domain = _.reduce(dims, function (widest, variable) {
var current = d.parcoords.yscale[variable].domain();
return [
Math.min(widest[0], current[0]),
Math.max(widest[1], current[1])
];
}, [Infinity, -Infinity]);
// Next, we change the domain of the variables that have to share scale.
_.each(dims, function (dim) {
d.parcoords.scale(dim, domain);
});
d.parcoords
.brushReset()
.updateAxes()
.render();
}
// function to be used as callback when data is requested
function loadData(data) {
setDimensions();
d.parcoords.data(data);
render();
if (ParCoords.sharedScaleVariables.length > 0) {
updateSharedAxes();
}
// if there is a row currently highlighted and it exists in the new dataset
// we want to ensure it is still highlighted
if (d.currentHighlightRow > -1) {
d.parcoords.highlight([d.parcoords.data()[d.currentHighlightRow]]);
}
}
// function to be used as callback when new varaibles
// are requested to be added on to existing data
function loadAdditionalData(data) {
setDimensions();
d.parcoords.data().forEach(function (d, i) {
_.forEach(data[i], function (val, key) {
d[key] = val;
});
});
render();
}
function highlightRow(itemIndex) {
d.currentHighlightRow = itemIndex;
if (d.currentHighlightRow > -1) {
d.parcoords.highlight([d.parcoords.data()[d.currentHighlightRow]]);
} else {
d.parcoords.unhighlight();
}
}
angular.element($window).bind('resize', resize);
$(document).ready(resize);
/// Scope extensions
// For some reason $scope.$watch(ParCoords.selectedVariables), doesn't
// work. So for now, I'll fall back to the more reliable broadcast
//meganism.
$scope.$on("ParCoords::selectedVariablesChanged", function () {
var dims = _.pluck(ParCoords.selectedVariables, "name"),
newVariables = _.difference(dims, d.parcoords.dimensions()),
missingVariables = _.difference(d.parcoords.dimensions(), dims),
existingVariables = _.intersection(d.parcoords.dimensions(), dims);
// Comparing variable names to existing variables and only requesting new ones
if (existingVariables.length === 0) {
DataSet.get(dims, loadData);
} else {
if (newVariables.length > 0) {
DataSet.get(newVariables, loadAdditionalData);
} else if (missingVariables.length > 0 || ParCoords.variablesToUpdate.length !== 0) {
if (ParCoords.variablesToUpdate.length !== 0) {
DataSet.get(ParCoords.variablesToUpdate, loadAdditionalData);
}
setDimensions();
render();
ParCoords.variablesToUpdate = [];
}
}
});
$scope.$on("ParCoords::brushedColorChanged", function (e, color) {
/*jslint unparam:true*/
d.parcoords.brushedColor(color);
d.parcoords.renderBrushed();
});
$scope.$on("DataSet::brushed", function (ev, brushed, method) {
if (method === "parcoords") {
return;
}
d.parcoords.brushReset();
if (brushed.length === 0) {
brushed = d.parcoords.data();
}
d.parcoords.brushed(brushed);
if (ParCoords.variableSorting !== "none") {
setDimensions();
d.parcoords.render();
}
d.parcoords.renderBrushed();
});
$scope.$on("ParCoords::variableSortingChanged", function () {
setDimensions();
d.parcoords.render();
});
$scope.$on("ParCoords::scaleSharingVariablesChanged", function () {
if (ParCoords.sharedScaleVariables.length > 0) {
updateSharedAxes();
} else {
d.parcoords
.autoscale()
.updateAxes()
.render();
}
});
$scope.$on("ParCoords::brushPredicateChanged", function () {
d.parcoords.brushPredicate(ParCoords.brushPredicate).renderBrushed();
});
$scope.$on("DataSet::dataLoaded", function (ev, data) {
d.parcoords.data(data);
render();
});
$scope.$on("DataSet::filtered", function (ev, filteredData) {
loadData(filteredData);
});
$scope.$on("Colors::changed", function (e, colors) {
function colorfn(d, i) {
return colors.hasOwnProperty(d.row) ? colors[d.row] : "#000";
}
d.parcoords.color(colorfn);
render();
});
$scope.$on("Opacity::changed", function (e, opacity) {
d.parcoords.alpha(opacity).render();
});
ParCoords.setHighlightFunction(highlightRow);
});
R.ICoVeR/inst/www/js/controllers/parcoordsvarsctrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint indent: 2*/
/*global angular */
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('ParCoordsVarsCtrl', function ($modal, $scope, ParCoords) {
'use strict';
$scope.parcoords = ParCoords;
$scope.brushPredicate = $scope.parcoords.brushPredicates[0];
$scope.variableSorting = "none";
$scope.noSharedScales = true;
$scope.openSelectionDialog = function () {
var dialog = $modal.open({
templateUrl: 'js/templates/selectvars.html',
size: 'sm',
controller: 'VariableSelectionCtrl',
resolve: {
variables: function () {
return $scope.parcoords.variables;
},
selected: function () {
return $scope.parcoords.selectedVariables;
}
}
});
dialog.result.then($scope.parcoords.updateSelectedVariables);
};
$scope.$watch('variableSorting', function (sortingMethod) {
$scope.parcoords.updateSortingMethod(sortingMethod);
});
$scope.openScaleBindDialog = function () {
var dialog = $modal.open({
templateUrl: 'js/templates/selectvars.html',
size: 'sm',
controller: 'VariableSelectionCtrl',
resolve: {
variables: function () {
return $scope.parcoords.selectedVariables;
},
selected: function () {
return $scope.parcoords.sharedScaleVariables;
}
}
});
dialog.result.then(function (variables) {
$scope.parcoords.shareScales(variables);
$scope.noSharedScales = variables.length === 0;
});
};
$scope.resetScales = function () {
$scope.parcoords.resetScales();
$scope.noSharedScales = true;
};
$scope.$watch("brushPredicate", function (newPredicate) {
$scope.parcoords.updateBrushPredicate(newPredicate);
});
});
R.ICoVeR/inst/www/js/controllers/plotctrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint indent: 2, nomen: true */
/*global angular, _, d3 */
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('PlotCtrl', function ($scope, DimRedPlot) {
'use strict';
$scope.analyses = [];
$scope.dimredplotWidth = "col-lg-12";
$scope.hideOptions = false;
$scope.sliding = {"left": 0};
function switchOptions() {
if ($scope.hideOptions) {
$scope.sliding = {"transform": "translate(0,0)"};
$scope.hideOptions = false;
} else {
$scope.sliding = {"transform": "translate(-90%, 0)"};
$scope.hideOptions = true;
}
}
$scope.switchOptions = function () {
switchOptions();
};
// Makes sure that the labels of points are no longer than 80px
function createWrappedLabels(points) {
var testText = d3.select("body").append("div").style("float", "left");
testText.style("font-size", "8px");
function wrap(d, i) {
/*jslint unparam:true*/
var textLength,
string,
desiredStringLength,
label = d.id;
if (d.label !== undefined) {
label = d.label;
}
testText.text(label);
textLength = testText.node().offsetWidth;
string = label;
desiredStringLength = Math.ceil(80 / textLength * string.length);
string = string.slice(0, desiredStringLength);
testText.text(string);
textLength = testText.node().clientWidth;
while (textLength > 80 && string.length > 0) {
string = string.slice(0, -1);
testText.text(string);
textLength = testText.node().clientWidth;
}
d.wrappedLabel = string;
}
points.forEach(wrap);
testText.remove();
}
function updatePlot(data) {
$scope.$apply(function () {
var index;
DimRedPlot.addProcessedData(data.method[0], data.processedData);
if (data.variableProjections !== undefined) {
createWrappedLabels(data.variableProjections);
}
if (data.individualProjections !== undefined) {
createWrappedLabels(data.individualProjections);
}
index = _.findIndex($scope.analyses, {'method': data.method});
if (index === -1) {
data.plotIdx = $scope.analyses.length;
$scope.analyses.push(data);
} else {
data.plotIdx = index;
$scope.analyses[index] = data;
}
$scope.dimredplotWidth = "col-lg-" + (12 / $scope.analyses.length);
if ($scope.analyses.length > 1) {
if (!$scope.hideOptions) {
switchOptions();
}
}
});
$scope.$broadcast("DimRedPlot::resize", $scope.analyses.length);
}
$scope.$on("Analytics::dimensionalityReduced", function (ev, method, session) {
/*jslint unparam: true */
session.getObject(updatePlot);
});
});
R.ICoVeR/inst/www/js/controllers/tagctrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint indent: 2, nomen: true */
/*global angular, _ */
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('TagCtrl', function ($scope, DataSet, Tag) {
'use strict';
// modify tag:
$scope.tags = [];
$scope.itemsBrushed = false;
$scope.modifyTag = "";
$scope.modifyTagExists = false;
$scope.placeholder = "selection1";
function checkIfMofidyTagExists() {
$scope.modifyTagExists = _.some($scope.tags, function (tag) {
return tag === $scope.modifyTag;
});
}
$scope.$on("Tag::tagsLoaded", function () {
$scope.tags = Tag.tags();
$scope.selectedTags = _.filter($scope.selectedTags, function (selectedTag) {
return _.some($scope.tags, function (tag) {
return selectedTag === tag;
});
});
checkIfMofidyTagExists();
});
$scope.$watch("modifyTag", function () {
checkIfMofidyTagExists();
});
$scope.createTag = function () {
Tag.storeTag($scope.modifyTag);
};
$scope.addToTag = function () {
Tag.appendToTag($scope.modifyTag);
};
// select tags:
$scope.dataFiltered = false;
$scope.filteringInProgress = false;
$scope.selectedTags = [];
$scope.enableDeselect = false;
$scope.removeTags = function () {
Tag.removeTags($scope.selectedTags);
};
$scope.selectTagged = function () {
Tag.selectTagged($scope.selectedTags);
};
$scope.deselectTags = function () {
Tag.selectTagged([]);
$scope.enableDeselect = false;
};
$scope.keepSelected = function () {
$scope.selectTagged();
$scope.filteringInProgress = true;
DataSet.filter(DataSet.FilterMethod.KEEP);
};
$scope.removeSelected = function () {
$scope.selectTagged();
$scope.filteringInProgress = true;
DataSet.filter(DataSet.FilterMethod.REMOVE);
};
$scope.reloadData = function () {
DataSet.filter(DataSet.FilterMethod.RESET);
};
$scope.$on('DataSet::loaded', function () {
$scope.dataFiltered = false;
$scope.tags = Tag.tags();
});
$scope.$on('DataSet::filtered', function () {
$scope.filteringInProgress = false;
$scope.dataFiltered = DataSet.filtered();
Tag.removeNonPresentTags();
});
$scope.$on('DataSet::brushed', function (e, rows, method) {
/*jslint unparam: true*/
$scope.enableDeselect = method === "tag";
$scope.itemsBrushed = rows.length > 0;
});
});
R.ICoVeR/inst/www/js/controllers/themectrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint indent: 2 */
/*global angular, $ */
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('ThemeCtrl', function ($scope, ParCoords) {
'use strict';
var link = $('#maincss');
$scope.theme = 'light';
$scope.$watch('theme', function (newTheme) {
var url = 'css/' + newTheme + '.css';
if (link.attr('href') !== url) {
link.attr('href', url);
}
ParCoords.changeTheme(newTheme);
});
});
R.ICoVeR/inst/www/js/controllers/variableselectionctrl.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint indent: 2 */
/*global angular */
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.controllers')
.controller('VariableSelectionCtrl', function ($scope, $modalInstance, variables, selected) {
'use strict';
$scope.variables = variables;
// https://stackoverflow.com
// /questions/21379173/angularjs-ui-modal-and-select-doesnt-update-the-scope-values
$scope.selected = {
variables: selected
};
$scope.ok = function () {
$modalInstance.close($scope.selected.variables);
};
$scope.cancel = function () {
$modalInstance.dismiss();
};
});
R.ICoVeR/inst/www/js/services/analytics.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint todo:true, nomen: true, indent: 2 */
/*global angular, ocpu, _ */
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.services')
.service('Analytics', function ($rootScope, DataSet) {
'use strict';
var d = {
clusterMethods: [],
dimRedMethods: []
};
/*jslint unparam: true */
$rootScope.$on("App::configurationLoaded", function (ev, appConfig) {
d.clusterMethods = _.reduce(_.keys(appConfig.cluster), function (methods, method) {
methods.push({ name: method, args: appConfig.cluster[method] });
return methods;
}, []);
$rootScope.$broadcast("Analytics::clusterMethodsAvailable", d.clusterMethods);
d.dimRedMethods = _.reduce(_.keys(appConfig.dimred), function (methods, method) {
var cfg = appConfig.dimred[method];
cfg.name = method;
methods.push(cfg);
return methods;
}, []);
$rootScope.$broadcast("Analytics::dimRedMethodsAvailable", d.dimRedMethods);
});
/*jslint unparam: false */
return {
clusterMethods: function () {
return d.clusterMethods;
},
dimRedMethods: function () {
return d.dimRedMethods;
},
cluster: function (method, variables, args, id) {
var fnArgs = {
vars: variables,
identifier: id
};
if (DataSet.rows()) {
fnArgs.rows = DataSet.rows();
}
_.each(_.keys(args), function (key) {
fnArgs[key] = args[key];
});
ocpu.call("cluster." + method, fnArgs, function () {
$rootScope.$broadcast("Analytics::dataUpdated", id);
});
},
reduce: function (method, variables) {
var fnArgs = {
vars: variables
};
if (DataSet.rows()) {
fnArgs.rows = DataSet.rows();
}
ocpu.call("dimred." + method, fnArgs, function (session) {
$rootScope.$broadcast("Analytics::dimensionalityReduced", method, session);
});
}
};
});
R.ICoVeR/inst/www/js/services/assert.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint todo:true, unparam: true, nomen: true, indent: 2 */
/*global angular */
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.services')
.service('assert', function () {
'use strict';
return {
strictEqual: function (actual, expected, message) {
var sEqual = (actual === expected),
msg = "Expected strict equality";
msg += (message !== undefined) ? ": " + message : "";
if (!sEqual) { throw new Error(msg); }
},
notStrictEqual: function (actual, expected, message) {
var sNotEqual = (actual !== expected),
msg = "Expected strict unequality";
msg += (message !== undefined) ? ": " + message : "";
if (!sNotEqual) { throw new Error(msg); }
}
};
});
R.ICoVeR/inst/www/js/services/color.js deleted 100644 → 0
View file @ f9ef00c0
/*jslint indent: 2, white: false, nomen: true */
/*global angular, _, d3 */
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.services')
.service('Color', function ($rootScope, DataSet, R) {
'use strict';
var d = {
dataSchema: undefined,
coloring: {
schemeName: undefined,
scheme: undefined,
method: undefined,
colorFn: undefined,
variable: undefined
},
schemes: {
numeric: {
value: {
blue_to_brown: ["steelblue", "brown"],
blue_to_yellow: ["blue", "yellow"],
cool: ["#00FFFF", "magenta"]
},
decile: {
yellow_to_red: d3.colorbrewer.YlOrRd[10],
yellow_to_green: d3.colorbrewer.YlGn[10],
blue_to_green: d3.colorbrewer.BuGn[10],
blue_to_purple: d3.colorbrewer.BuPu[10],
blues: d3.colorbrewer.Blues[10]
}
},
factor: {
value: {
"paired (12 colors)": d3.colorbrewer.Paired[12],
"set3 (12 colors)": d3.colorbrewer.Set3[12],
"category A (20 colors)": d3.scale.category20().range(),
"category B (20 colors)": d3.scale.category20b().range(),
"category C (20 colors)": d3.scale.category20c().range(),
"red_yellow_blue (11 colors)": d3.colorbrewer.RdYlBu[11]
// the qualitiative set will calulate the number of clusters before application
// qualitative_set: [] //rainbow_hcl(30, c = 50, l = 70, start = 0, end = 360*(30-1)/30)
}
}
}
},
cfg = {
numeric: {
Value: _.keys(d.schemes.numeric.value),
Decile: _.keys(d.schemes.numeric.decile)
//"Z-score" = c("RedToBlue", "Spectral")
},
factor: {
Value: _.keys(d.schemes.factor.value)
}
};
function variableType(variable) {
return _.result(_.find(d.dataSchema, { name: variable }), 'type');
}
function colorFactorValue(colorVariable, colorScheme) {
DataSet.get([colorVariable], function (data) {
var domain = _.pluck(_.uniq(data, colorVariable), colorVariable),
colored = {};
d.coloring.colorFn = d3.scale.ordinal();
d.coloring.colorFn
.domain(domain)
.range(d.schemes.factor.value[colorScheme]);
_.each(data, function (datum) {
colored[datum.row] = d.coloring.colorFn(datum[colorVariable]);
});
d.coloring.scheme = d.schemes.factor.value[colorScheme];
$rootScope.$broadcast("Colors::changed", colored);
});
}
function colorNumericValue(colorVariable, colorScheme) {
DataSet.get([colorVariable], function (data) {
var domain = d3.extent(data, function (datum) { return datum[colorVariable]; }),
colored = {};
d.coloring.colorFn = d3.scale.linear();
d.coloring.colorFn
.domain(domain)
.range(d.schemes.numeric.value[colorScheme])
.interpolate(d3.interpolateLab);
_.each(data, function (datum) {
colored[datum.row] = d.coloring.colorFn(datum[colorVariable]);
});
d.coloring.scheme = d.schemes.numeric.value[colorScheme];
$rootScope.$broadcast("Colors::changed", colored);
});
}
// Puts 10 percent of the data items, ordered by color variabel in the same
// bin.
function colorNumericDecile(colorVariable, colorScheme) {
DataSet.get([colorVariable], function (data) {
var colored = {},
binSize = Math.round(data.length / 10),
currentBin = 0,
currentBinSize = 0,
lastValue,
colorStepValues = [];
data.sort(function (a, b) {
return +a[colorVariable] - +b[colorVariable];
});
colorScheme = d.schemes.numeric.decile[colorScheme];
_.each(data, function (row) {
var value = row[colorVariable];
if (currentBinSize >= binSize && currentBin < 9 && value !== lastValue) {
currentBin = currentBin + 1;
currentBinSize = 0;
colorStepValues.push((value + lastValue) / 2);
}
currentBinSize = currentBinSize + 1;
lastValue = value;
colored[row.row] = colorScheme[currentBin];
});
d.coloring.colorFn = function (value) {
var bin = 0;
_.each(colorStepValues, function (stepValue) {
if (value > stepValue) {
bin += 1;
} else {
return;
}
});
return colorScheme[bin];
};
d.coloring.scheme = d.schemes.numeric.decile[colorScheme];
$rootScope.$broadcast("Colors::changed", colored);
});
}
function colorNumeric(colorVariable, colorMethod, colorScheme) {
switch (colorMethod) {
case "Value":
colorNumericValue(colorVariable, colorScheme);
break;
case "Decile":
colorNumericDecile(colorVariable, colorScheme);
break;
case "Z-score":
break;
default:
throw "Unsupported color method:" + colorMethod;
}
}
function colorFactor(colorVariable, colorMethod, colorScheme) {
switch (colorMethod) {
case "Value":
colorFactorValue(colorVariable, colorScheme);
break;
default:
throw "Unsupported color method:" + colorMethod;
}
}
function colorManual(colorScheme) {
var data = DataSet.data(),
rowColors = {};
d.coloring.colorFn = function () {
return "steelblue";
};
_.forEach(data, function (row) {
rowColors[row.row] = "steelblue";
});
d.coloring.scheme = d.schemes.factor.value[colorScheme];
DataSet.addVariable("Manual selection", rowColors, "factor", "Colors", "steelblue");
$rootScope.$broadcast("Colors::changed", rowColors);
}
function color(variable, colorMethod, colorScheme) {
var type = variableType(variable);
d.coloring.variable = variable;
d.coloring.method = colorMethod;
d.coloring.schemeName = colorScheme;
if (R.is.factor(type)) {
if (variable === "Manual selection") {
colorManual(colorScheme);
} else {
colorFactor(variable, colorMethod, colorScheme);
}
} else if (R.is.numeric(type)) {
colorNumeric(variable, colorMethod, colorScheme);
} else {
throw type + " is an unsupported data type";
}
}
/*jslint unparam: true */
$rootScope.$on("DataSet::schemaLoaded", function (ev, schema) {
d.dataSchema = schema;
});
/*jslint unparam: false */
$rootScope.$on('DataSet::analyticsUpdated', function (e, analyticsSchema) {
/*jslint unparam:true*/
if (analyticsSchema.type !== "numeric" && d.coloring.variable === undefined) {
return; // We do not want automatic colouring on clustering
}
if (d.coloring.variable === undefined) {
d.coloring.method = "Value";
d.coloring.schemeName = "blue_to_brown";
}
if (d.coloring.variable === undefined || d.coloring.variable === analyticsSchema.name) {
color(analyticsSchema.name, d.coloring.method, d.coloring.schemeName);
}
});
$rootScope.$on("DataSet::initialDataLoaded", function () {
DataSet.addVariable("Manual selection", {}, "factor", "Colors", "steelblue");
});
return {
configuration: function () {
return cfg;
},
color: color,
colorScheme: function () {
return d.coloring.scheme;
},
colorSchemeName: function () {
return d.coloring.schemeName;
},
colorMethod: function () {
return d.coloring.method;
},
colorFn: function () {
return d.coloring.colorFn;
},
colorVariable: function () {
return d.coloring.variable;
},
colorBrushed: function (color) {
var rowColors = {};
DataSet.get(["Manual selection"], function (rows) {
_.forEach(rows, function (row) {
rowColors[row.row] = row["Manual selection"];
});
});
_.forEach(DataSet.brushed(), function (row) {
rowColors[row.row] = color;
});
d.coloring.variable = "Manual selection";
d.coloring.colorFn = function (colorVal) {
return colorVal; // The values of this variable are actually colors
};
DataSet.addVariable("Manual selection", rowColors, "factor", "Colors", "steelblue");
$rootScope.$broadcast("Colors::changed", rowColors);
},
opacity: function (value) {
$rootScope.$broadcast("Opacity::changed", value);
}
};
});
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/*jslint todo:true, nomen: true, white: false, indent: 2, unparam: true */
/*global angular, _, ocpu*/
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.services')
.service('DataSet', function ($rootScope, $http, assert, OpenCPU) {
'use strict';
var d = {
id: undefined,
data: undefined,
brushed: [],
backend: {
schema: undefined,
schemaIndex: undefined,
rows: undefined,
analytics: {
clusterings: {},
summaries: {}
}
}
};
function updateSchema(schema) {
d.backend.schema = schema;
// This adds a property that determines whether the variable is analysable in the R backend. This is necessary
// because some variables are only calculated in the Javascript.
_.forEach(d.backend.schema, function (variable) {
variable.analysable = true;
});
d.backend.schemaIndex = _.indexBy(schema, 'name');
$rootScope.$broadcast("DataSet::schemaLoaded", schema);
}
// Initialize the application as soon as the Dataset service is initialized and receive
// the required information to configure and further bootstrap the front end.
OpenCPU.json("app.init", {timestamp: Date.now()}, function (session, cfg) {
d.data = cfg.data;
updateSchema(cfg.data.schema);
$rootScope.$broadcast("App::configurationLoaded", cfg);
});
$rootScope.$on("ParCoords::brushPredicateChanged", function (ev, predicate) {
d.brushPredicate = predicate;
});
function addVariable(name, rows, type, group, missingReplacement) {
var variableSchema = {name: name, type: type, group: group, group_type: group, analysable: false},
rowArray = [],
value,
newVariable = false;
if (d.backend.schemaIndex[name] === undefined) {
d.backend.schema.push(variableSchema);
d.backend.schemaIndex[name] = variableSchema;
newVariable = true;
}
d.data.full.forEach(function (datum, idx) {
d.data.full[idx][name] = rows[datum.row];
});
if (d.data.filtered !== undefined) {
d.data.filtered.forEach(function (datum, idx) {
d.data.filtered[idx][name] = rows[datum.row];
});
}
if (newVariable) {
$rootScope.$broadcast('DataSet::schemaLoaded', d.backend.schema);
}
if (group === "Analytics") {
$rootScope.$broadcast('DataSet::analyticsUpdated', variableSchema);
}
// Tags need to be added to the actual database
// Preferably, R should get a function addVariable and the DataSet should not have to care what
// the group is of the variable we want to add. This would however require some extra work in R.
if (group === "Tags") {
_.each(d.data.full, function (row) {
value = rows[row.row];
if (value === undefined) {
value = missingReplacement;
}
rowArray.push(value);
});
OpenCPU.call("data.addTag", {timestamp: Date.now(), name: name, data: rowArray});
}
return variableSchema;
}
function removeVariable(name) {
var variableIdx = _.findIndex(d.backend.schema, "name", name),
group;
if (variableIdx === -1) {
return;
}
group = d.backend.schema[variableIdx].group;
d.backend.schema.splice(variableIdx, 1);
delete d.backend.schemaIndex[name];
$rootScope.$broadcast('DataSet::schemaLoaded', d.backend.schema);
if (group === "Tags") {
OpenCPU.call("data.removeTag", {timestamp: Date.now(), name: name});
}
}
// Listen to the analytics service to store the results of various
// analytical actions.
$rootScope.$on("Analytics::dataUpdated", function (ev, identifier) {
if (!d.backend.schemaIndex.hasOwnProperty(identifier)) {
// We send the current timestamp as arg to avoid caching to happen here
OpenCPU.json("data.schema", {timestamp: Date.now()}, function (session, schema) {
updateSchema(schema);
$rootScope.$broadcast("DataSet::analyticsUpdated", d.backend.schemaIndex[identifier]);
});
} else {
$rootScope.$broadcast("DataSet::analyticsUpdated", d.backend.schemaIndex[identifier]);
}
});
function processReceivedData(data) {
d.data.filtered = undefined; // Reset filtered data.
if (d.data.full === undefined) {
d.data.full = data;
d.data.full.index = {};
_.each(data, function (datum, i) {
d.data.full.index[datum.row] = i;
});
$rootScope.$broadcast("DataSet::initialDataLoaded");
} else {
// For each item we retrieved
_.each(data, function (datum) {
// If the item doesn't exist yet in the full data set, we'll have to
// add it.
if (d.data.full.index[datum.row] === undefined) {
d.data.full.index[datum.row] = d.data.full.length;
d.data.full.push(datum);
}
// Update the item in the full data set.
var index = d.data.full.index[datum.row],
dataItem = d.data.full[index],
keys = _.keys(datum);
_.each(keys, function (key) {
dataItem[key] = datum[key];
});
d.data.full[index] = dataItem; // Not sure if this is required
});
}
}
function dataFiltered() {
return d.backend.rows !== undefined && d.backend.rows.length > 0;
}
function filterData() {
if (!dataFiltered) { throw "Trying to filter unfiltered data."; }
var filtered = d.data.filtered || [];
// Recreate the filtered set of rows
_.each(d.backend.rows, function (row) {
var index = d.data.full.index[row];
filtered.push(d.data.full[index]);
});
return filtered;
}
function currentDataSet() {
if (dataFiltered()) {
if (!d.data.filtered) { d.data.filtered = filterData(); }
return d.data.filtered.slice();
}
if (d.data !== undefined && d.data.full !== undefined) {
return d.data.full.slice();
}
return [];
}
function changeBrushed(rows, method) {
d.brushed = rows;
$rootScope.$broadcast("DataSet::brushed", rows, method);
}
return {
FilterMethod: { KEEP: 'KEEP', REMOVE: 'REMOVE', RESET: 'RESET' },
/**
* Returns the row ids of the currently filtered rows or undefined if no
* filtering was applied (meaning all rows will loaded when using get).
*/
rows: function () {
return d.backend.rows;
},
/**
* Returns the full data set as it is currently loaded, this takes filtering into account.
*/
data: currentDataSet,
schema: function () {
return d.backend.schema.slice();
},
brushed: function () {
if (d.brushed === undefined) {
return [];
}
return d.brushed;
},
addVariable: addVariable,
removeVariable: removeVariable,
// Returns the data values for given variables.
// @param variables - a list of strings, containing the names of the
// variables to be loaded.
// @param callback - a function to be executed once data has been successfully loaded
get: function (variables, callback) {
var args = {},
availableVariables;
// TODO: Create a unique id for each requests. When a new request comes
// in, check if there is an ongoing requests which encompasses all
// variables in the new request. If so, add the callback to the
// list of callbacks for this request. Otherwise, remove already
// requested variables from the list (they will come in with the
// ongoing request) and place a new request with the remaining
// variables. The callback is called only when the remaining
// variables are loaded.
// @see _.uniqueId
if (d.data.full !== undefined && d.data.full.length > 0) {
availableVariables = _.keys(d.data.full[0]);
variables = _.difference(variables, availableVariables);
}
if (variables.length > 0) {
args.variables = variables;
// Always get the full column to avoid synchronization problems
// related to filtering
//args.rows = d.backend.rows;
OpenCPU.json("data.get", args, function (session, data) {
processReceivedData(data);
callback(currentDataSet());
});
} else {
// All variables are alread there, just directly return the data.
callback(currentDataSet());
}
},
filter: function (filterMethod) {
if (filterMethod === this.FilterMethod.RESET) {
d.backend.rows = undefined;
$rootScope.$broadcast("DataSet::filtered", currentDataSet());
return;
}
if (d.brushed.length === 0) { throw "ERROR, filtering while nothing is brushed"; }
if (filterMethod === this.FilterMethod.KEEP) {
d.backend.rows = _.pluck(d.brushed, "row");
} else {
var toRemove = _.indexBy(_.pluck(d.brushed, "row"));
d.backend.rows = d.backend.rows || _.pluck(d.data.full, "row");
d.backend.rows = _.filter(d.backend.rows, function (d) {
return toRemove[d] === undefined;
});
}
changeBrushed([], "filter");
d.data.filtered = undefined;
$rootScope.$broadcast("DataSet::filtered", currentDataSet());
},
filtered: function () {
return d.backend.rows && d.backend.rows.length > 0;
},
brush: changeBrushed
};
});
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/*jslint white: false, indent: 2, nomen: true */
/*global angular, ocpu, _ */
/*
ICoVeR - Interactive Contig-bin Verification and Refinement
Copyright 2015 Luxembourg Institute of Science and technology. All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
angular.module('contigBinningApp.services')
.service('OpenCPU', function ($http) {
'use strict';
// For testing without having to re-install the R-plugin over and over again
// enable the following line, adjust the path, and run:
// rparcoords/inst/www $ python -m SimpleHTTPServer
//
// NOTE: Make sure that this line is disabled when you run gulp to generate
// the minimized version!
//ocpu.seturl("//localhost/ocpu/user/bertjan/library/ICoVeR/R", false);
function asJson(callback) {
return function (session) {
$http({method: 'GET', url: session.loc + "R/.val/json?auto_unbox=true"})
.success(_.partial(callback, session));
};
}
return {
call: function (fn, args, cb) {
ocpu.call(fn, args, cb);
},
json: function (fn, args, cb) {
ocpu.call(fn, args, asJson(cb));
}
};
});
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<form role="form" class="form-horizontal" ng-controller="DimRedDisplayCtrl">
<div class="form-group">
<label class="col-sm-3 control-label adjusted-right-padding text-right">Cluster count:</label>
<div class="col-sm-9 no-left-padding">
<select class="form-control input-sm"
ng-model="cluster"
ng-options="cluster.label for cluster in clusters">
</select>
</div>
</div>
</form>
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