giant_limma_analysis: src/heatMapClustering.R annotate

annotate src/heatMapClustering.R @ 0:f274c8d45613 draft

"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"

author	vandelj
date	Fri, 26 Jun 2020 09:43:41 -0400
parents
children

rev	line source
0 f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	1 # A command-line interface to plot heatmap based on expression or diff. exp. analysis
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	2 # written by Jimmy Vandel
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	3 # one of these arguments is required:
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	4 #
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	5 #
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	6 initial.options <- commandArgs(trailingOnly = FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	7 file.arg.name <- "--file="
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	8 script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)])
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	9 script.basename <- dirname(script.name)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	10 source(file.path(script.basename, "utils.R"))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	11 source(file.path(script.basename, "getopt.R"))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	12
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	13 #addComment("Welcome R!")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	14
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	15 # setup R error handling to go to stderr
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	16 options( show.error.messages=F, error = function () { cat(geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	17
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	18 # we need that to not crash galaxy with an UTF8 error on German LC settings.
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	19 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	20 loc <- Sys.setlocale("LC_NUMERIC", "C")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	21
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	22 #get starting time
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	23 start.time <- Sys.time()
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	24
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	25
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	26 options(stringAsfactors = FALSE, useFancyQuotes = FALSE, OutDec=".")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	27
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	28 #get options
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	29 args <- commandArgs()
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	30
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	31 # get options, using the spec as defined by the enclosed list.
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	32 # we read the options from the default: commandArgs(TRUE).
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	33 spec <- matrix(c(
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	34 "expressionFile", "x", 1, "character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	35 "diffAnalyseFile", "x", 1, "character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	36 "factorInfo","x", 1, "character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	37 "genericData","x", 0, "logical",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	38 "comparisonName","x",1,"character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	39 "comparisonNameLow","x",1,"character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	40 "comparisonNameHigh","x",1,"character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	41 "filterInputOutput","x", 1, "character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	42 "FCthreshold","x", 1, "double",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	43 "pvalThreshold","x", 1, "double",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	44 "geneListFiltering","x",1,"character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	45 "clusterNumber","x",1,"integer",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	46 "maxRows","x",1,"integer",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	47 "sampleClusterNumber","x",1,"integer",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	48 "dataTransformation","x",1,"character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	49 "distanceMeasure","x",1,"character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	50 "aggloMethod","x",1,"character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	51 "personalColors","x",1,"character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	52 "sideBarColorPalette","x",1,"character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	53 "format", "x", 1, "character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	54 "quiet", "x", 0, "logical",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	55 "log", "x", 1, "character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	56 "outputFile" , "x", 1, "character"),
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	57 byrow=TRUE, ncol=4)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	58 opt <- getoptLong(spec)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	59
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	60 # enforce the following required arguments
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	61 if (is.null(opt$log)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	62 addComment("[ERROR]'log file' is required")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	63 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	64 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	65 addComment("[INFO]Start of R script",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	66 if (is.null(opt$format)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	67 addComment("[ERROR]'output format' is required",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	68 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	69 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	70 if (is.null(opt$outputFile)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	71 addComment("[ERROR]'output file' is required",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	72 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	73 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	74
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	75 if(is.null(opt$expressionFile) && !is.null(opt$genericData)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	76 addComment("[ERROR]generic data clustering is based on expression clustering",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	77 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	78 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	79
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	80 if (is.null(opt$clusterNumber) \|\| opt$clusterNumber<2) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	81 addComment("[ERROR]valid genes clusters number is required",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	82 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	83 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	84
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	85 if (is.null(opt$sampleClusterNumber) \|\| opt$sampleClusterNumber<1) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	86 addComment("[ERROR]valid samples clusters number is required",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	87 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	88 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	89
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	90 if (is.null(opt$dataTransformation)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	91 addComment("[ERROR]data transformation option is required",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	92 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	93 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	94
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	95 if (is.null(opt$distanceMeasure)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	96 addComment("[ERROR]distance measure option is required",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	97 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	98 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	99
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	100 if (is.null(opt$aggloMethod)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	101 addComment("[ERROR]agglomeration method option is required",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	102 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	103 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	104
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	105 if (is.null(opt$maxRows) \|\| opt$maxRows<2) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	106 addComment("[ERROR]valid plotted row number is required",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	107 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	108 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	109
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	110 if (!is.null(opt[["comparisonName"]]) && nchar(opt[["comparisonName"]])==0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	111 addComment("[ERROR]you have to specify comparison",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	112 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	113 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	114
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	115 if (!is.null(opt$comparisonNameLow) && nchar(opt$comparisonNameLow)==0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	116 addComment("[ERROR]you have to specify comparisonLow",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	117 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	118 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	119
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	120 if (!is.null(opt$comparisonNameHigh) && nchar(opt$comparisonNameHigh)==0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	121 addComment("[ERROR]you have to specify comparisonHigh",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	122 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	123 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	124
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	125 if (is.null(opt$genericData) && (!is.null(opt$comparisonNameLow) \|\| !is.null(opt$comparisonNameHigh))){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	126 addComment("[ERROR]comparisonLow and comparisonHigh can be specified only with generic data",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	127 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	128 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	129
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	130 if (!is.null(opt$genericData) && !is.null(opt[["comparisonName"]])){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	131 addComment("[ERROR]basic comparison cannot be specified for generic data",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	132 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	133 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	134
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	135 if ((!is.null(opt[["comparisonName"]]) \|\| !is.null(opt$comparisonNameLow) \|\| !is.null(opt$comparisonNameHigh)) && is.null(opt$diffAnalyseFile)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	136 addComment("[ERROR]'diff. exp. analysis file' is required",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	137 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	138 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	139
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	140 if (!is.null(opt$genericData) && !is.null(opt$diffAnalyseFile) && is.null(opt$comparisonNameLow) && is.null(opt$comparisonNameHigh)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	141 addComment("[ERROR]Missing comparison information for filtering",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	142 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	143 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	144
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	145 if ((!is.null(opt$FCthreshold) \|\| !is.null(opt$pvalThreshold)) && (is.null(opt[["comparisonName"]]) && is.null(opt$comparisonNameLow) && is.null(opt$comparisonNameHigh))) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	146 addComment("[ERROR]'comparisons' are missing for filtering",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	147 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	148 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	149
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	150 if ((!is.null(opt$FCthreshold) \|\| !is.null(opt$pvalThreshold)) && !is.null(opt$geneListFiltering)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	151 addComment("[ERROR]Cannot have two filtering strategies",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	152 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	153 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	154
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	155 verbose <- if (is.null(opt$quiet)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	156 TRUE
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	157 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	158 FALSE}
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	159
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	160 addComment("[INFO]Parameters checked!",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	161
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	162 addComment(c("[INFO]Working directory: ",getwd()),TRUE,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	163 addComment(c("[INFO]Command line: ",args),TRUE,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	164
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	165 #directory for plots and HTML
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	166 dir.create(file.path(getwd(), "plotDir"))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	167 dir.create(file.path(getwd(), "plotLyDir"))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	168
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	169 #silent package loading
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	170 suppressPackageStartupMessages({
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	171 library("plotly")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	172 library("dendextend")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	173 #library("ggdendro")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	174 #library("plyr")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	175 library("ggplot2")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	176 library("heatmaply")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	177 library("circlize")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	178 #library("RColorBrewer")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	179 #source("https://bioconductor.org/biocLite.R")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	180 #biocLite("ComplexHeatmap")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	181 library("ComplexHeatmap")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	182 #library("processx")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	183 })
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	184
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	185 expressionToCluster=!is.null(opt$expressionFile)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	186
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	187 #load input data files
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	188 if(expressionToCluster){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	189 #first expression data
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	190 expressionMatrix=read.csv(file=opt$expressionFile,header=F,sep="\t",colClasses="character")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	191 #remove first row to convert it as colnames (to avoid X before colnames with header=T)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	192 colNamesData=expressionMatrix[1,-1]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	193 expressionMatrix=expressionMatrix[-1,]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	194 #remove first colum to convert it as rownames
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	195 rowNamesData=expressionMatrix[,1]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	196 expressionMatrix=expressionMatrix[,-1]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	197 if(is.data.frame(expressionMatrix)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	198 expressionMatrix=data.matrix(expressionMatrix)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	199 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	200 expressionMatrix=data.matrix(as.numeric(expressionMatrix))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	201 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	202 dimnames(expressionMatrix)=list(rowNamesData,colNamesData)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	203
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	204 #check input files
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	205 if (!is.numeric(expressionMatrix)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	206 addComment("[ERROR]Expression data is not fully numeric!",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	207 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	208 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	209
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	210 addComment("[INFO]Expression data loaded and checked")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	211 addComment(c("[INFO]Dim of expression matrix:",dim(expressionMatrix)),T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	212 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	213
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	214 nbComparisons=0
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	215 nbColPerContrast=5
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	216 comparisonMatrix=NULL
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	217 comparisonMatrixInfoGene=NULL
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	218 #if available comparisons
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	219 if(!is.null(opt[["comparisonName"]])){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	220 #load results from differential expression analysis
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	221 #consider first row contains column names
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	222 comparisonMatrix=read.csv(file=opt$diffAnalyseFile,header=F,sep="\t")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	223 colnames(comparisonMatrix)=as.character(unlist(comparisonMatrix[1,]))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	224 #remove the second line also as it's information line (p-val,FDR.p-val,FC,logFC)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	225 comparisonMatrix=comparisonMatrix[-c(1,2),]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	226 #remove first and second colums, convert the first one as rownames
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	227 rownames(comparisonMatrix)=as.character(unlist(comparisonMatrix[,1]))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	228 #and save second column content that contain geneInfo
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	229 comparisonMatrixInfoGene=as.character(unlist(comparisonMatrix[,2]))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	230 names(comparisonMatrixInfoGene)=as.character(unlist(comparisonMatrix[,1]))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	231 comparisonMatrix=comparisonMatrix[,-c(1,2)]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	232
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	233 comparisonMatrix=matrix(as.numeric(as.matrix(comparisonMatrix)),ncol=ncol(comparisonMatrix),dimnames = dimnames(comparisonMatrix))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	234
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	235 if (ncol(comparisonMatrix)%%nbColPerContrast != 0) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	236 addComment("[ERROR]Diff. exp. data does not contain good number of columns per contrast, should contains in this order:p-val,FDR.p-val,FC,log2(FC) and t-stat",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	237 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	238 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	239
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	240 if(max(comparisonMatrix[,c(seq(1,ncol(comparisonMatrix),nbColPerContrast),seq(2,ncol(comparisonMatrix),nbColPerContrast))])>1 \|\| min(comparisonMatrix[,c(seq(1,ncol(comparisonMatrix),nbColPerContrast),seq(2,ncol(comparisonMatrix),nbColPerContrast))])<0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	241 addComment("[ERROR]Seem that diff. exp. data does not contain correct values for p-val and FDR.p-val columns, should be including in [0,1] interval",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	242 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	243 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	244
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	245 if (!is.numeric(comparisonMatrix)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	246 addComment("[ERROR]Diff. exp. data is not fully numeric!",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	247 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	248 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	249
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	250 if(expressionToCluster && length(setdiff(rownames(comparisonMatrix),rownames(expressionMatrix)))!=0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	251 addComment("[WARNING]All genes from diff. exp. file are not included in expression file",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	252 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	253
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	254 if(expressionToCluster && length(setdiff(rownames(expressionMatrix),rownames(comparisonMatrix)))!=0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	255 addComment("[WARNING]All genes from expression file are not included in diff. exp. file",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	256 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	257
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	258 addComment("[INFO]Diff. exp. analysis loaded and checked",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	259 addComment(c("[INFO]Dim of original comparison matrix:",dim(comparisonMatrix)),T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	260
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	261 #restrict to user specified comparisons
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	262 restrictedComparisons=unlist(strsplit(opt[["comparisonName"]],","))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	263 #should be improved to avoid selection of column names starting too similarly
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	264 colToKeep=which(unlist(lapply(colnames(comparisonMatrix),function(x)any(startsWith(x,restrictedComparisons)))))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	265 comparisonMatrix=matrix(comparisonMatrix[,colToKeep],ncol=length(colToKeep),dimnames = list(rownames(comparisonMatrix),colnames(comparisonMatrix)[colToKeep]))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	266
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	267 #get number of required comparisons
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	268 nbComparisons=ncol(comparisonMatrix)/nbColPerContrast
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	269
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	270 addComment(c("[INFO]Dim of effective filtering matrix:",dim(comparisonMatrix)),T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	271 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	272
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	273 #should be only the case with generic data
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	274 if(!is.null(opt$comparisonNameLow) \|\| !is.null(opt$comparisonNameHigh)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	275 #load generic data used for filtering
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	276 nbColPerContrast=1
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	277 #consider first row contains column names
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	278 comparisonMatrix=read.csv(file=opt$diffAnalyseFile,header=F,sep="\t")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	279 colnames(comparisonMatrix)=as.character(unlist(comparisonMatrix[1,]))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	280 #remove first colum, convert the first one as rownames
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	281 rownames(comparisonMatrix)=as.character(unlist(comparisonMatrix[,1]))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	282 comparisonMatrix=comparisonMatrix[-1,-1]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	283
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	284 comparisonMatrix=matrix(as.numeric(as.matrix(comparisonMatrix)),ncol=ncol(comparisonMatrix),dimnames = dimnames(comparisonMatrix))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	285
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	286 if (!is.numeric(comparisonMatrix)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	287 addComment("[ERROR]Filtering matrix is not fully numeric!",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	288 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	289 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	290
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	291 if(expressionToCluster && length(setdiff(rownames(comparisonMatrix),rownames(expressionMatrix)))!=0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	292 addComment("[WARNING]All genes from filtering file are not included in expression file",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	293 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	294
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	295 if(expressionToCluster && length(setdiff(rownames(expressionMatrix),rownames(comparisonMatrix)))!=0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	296 addComment("[WARNING]All genes from expression file are not included in filtering file",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	297 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	298
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	299 addComment("[INFO]Filtering file loaded and checked",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	300 addComment(c("[INFO]Dim of original filtering matrix:",dim(comparisonMatrix)),T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	301
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	302 #restrict to user specified comparisons
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	303 restrictedComparisons=c()
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	304 if(!is.null(opt$comparisonNameLow))restrictedComparisons=unique(c(restrictedComparisons,unlist(strsplit(opt$comparisonNameLow,","))))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	305 if(!is.null(opt$comparisonNameHigh))restrictedComparisons=unique(c(restrictedComparisons,unlist(strsplit(opt$comparisonNameHigh,","))))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	306
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	307 if (!all(restrictedComparisons%in%colnames(comparisonMatrix))){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	308 addComment("[ERROR]Selected columns in filtering file are not present in filtering matrix!",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	309 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	310 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	311 comparisonMatrix=matrix(comparisonMatrix[,restrictedComparisons],ncol=length(restrictedComparisons),dimnames = list(rownames(comparisonMatrix),restrictedComparisons))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	312
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	313 #get number of required comparisons
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	314 nbComparisons=ncol(comparisonMatrix)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	315
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	316 addComment(c("[INFO]Dim of effective filtering matrix:",dim(comparisonMatrix)),T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	317 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	318
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	319
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	320
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	321 factorInfoMatrix=NULL
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	322 if(!is.null(opt$factorInfo)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	323 #get group information
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	324 #load factors file
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	325 factorInfoMatrix=read.csv(file=opt$factorInfo,header=F,sep="\t",colClasses="character")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	326 #remove first row to convert it as colnames
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	327 colnames(factorInfoMatrix)=factorInfoMatrix[1,]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	328 factorInfoMatrix=factorInfoMatrix[-1,]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	329 #use first colum to convert it as rownames but not removing it to avoid conversion as vector in unique factor case
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	330 rownames(factorInfoMatrix)=factorInfoMatrix[,1]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	331
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	332 factorBarColor=colnames(factorInfoMatrix)[2]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	333
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	334 if(ncol(factorInfoMatrix)>2){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	335 addComment("[ERROR]Factors file should not contain more than 2 columns",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	336 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	337 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	338
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	339 #factor file is used for color band on heatmap, so all expression matrix column should be in the factor file
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	340 if(expressionToCluster && length(setdiff(colnames(expressionMatrix),rownames(factorInfoMatrix)))!=0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	341 addComment("[ERROR]Missing samples in factor file",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	342 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	343 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	344
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	345 #factor file is used for color band on heatmap, so all comparison matrix column should be in the factor file
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	346 if(!expressionToCluster && length(setdiff(colnames(comparisonMatrix),rownames(factorInfoMatrix)))!=0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	347 addComment("[ERROR]Missing differential contrasts in factor file",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	348 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	349 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	350
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	351 addComment("[INFO]Factors OK",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	352 addComment(c("[INFO]Dim of factorInfo matrix:",dim(factorInfoMatrix)),T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	353 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	354
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	355 if(!is.null(opt$personalColors)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	356 ##parse personal colors
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	357 personalColors=unlist(strsplit(opt$personalColors,","))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	358 if(length(personalColors)==2){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	359 ##add medium color between two to get three colors
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	360 personalColors=c(personalColors[1],paste(c("#",as.character(as.hexmode(floor(apply(col2rgb(personalColors),1,mean))))),collapse=""),personalColors[2])
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	361 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	362 if(length(personalColors)!=3){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	363 addComment("[ERROR]Personalized colors doesn't contain enough colors",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	364 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	365 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	366
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	367 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	368
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	369
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	370 if(!is.null(opt$filterInputOutput) && opt$filterInputOutput=="input"){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	371 #filter input data
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	372
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	373 if(is.null(opt$geneListFiltering)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	374 #filtering using stat thresholds
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	375 #rowToKeep=intersect(which(comparisonMatrix[,seq(2,ncol(comparisonMatrix),4)]<=opt$pvalThreshold),which(abs(comparisonMatrix[,seq(4,ncol(comparisonMatrix),4)])>=log2(opt$FCthreshold)))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	376 if(is.null(opt$genericData)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	377 #diff. expression matrix
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	378 rowToKeep=names(which(unlist(apply(comparisonMatrix,1,function(x)length(intersect(which(x[seq(2,length(x),nbColPerContrast)]<opt$pvalThreshold),which(abs(x[seq(4,length(x),nbColPerContrast)])>log2(opt$FCthreshold))))!=0))))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	379 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	380 #generic filtering matrix
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	381 rowToKeep=rownames(comparisonMatrix)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	382 if(!is.null(opt$comparisonNameLow)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	383 restrictedLowComparisons=unlist(strsplit(opt$comparisonNameLow,","))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	384 rowToKeep=intersect(rowToKeep,names(which(unlist(apply(comparisonMatrix,1,function(x)length(which(x[restrictedLowComparisons]>opt$FCthreshold))!=0)))))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	385 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	386 if(!is.null(opt$comparisonNameHigh)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	387 restrictedHighComparisons=unlist(strsplit(opt$comparisonNameHigh,","))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	388 rowToKeep=intersect(rowToKeep,names(which(unlist(apply(comparisonMatrix,1,function(x)length(which(x[restrictedHighComparisons]<opt$pvalThreshold))!=0)))))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	389 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	390 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	391 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	392 #filtering using user gene list
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	393 geneListFiltering=read.csv(opt$geneListFiltering,as.is = 1,header=F)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	394 rowToKeep=unlist(c(geneListFiltering))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	395 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	396
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	397 if(!is.null(comparisonMatrix) && !all(rowToKeep%in%rownames(comparisonMatrix))){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	398 #should arrive only with user gene list filtering with diff.exp. results clustering
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	399 addComment("[WARNING] some genes of the user defined list are not in the diff. exp. input file",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	400 rowToKeep=intersect(rowToKeep,rownames(comparisonMatrix))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	401 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	402
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	403 if(expressionToCluster && !all(rowToKeep%in%rownames(expressionMatrix))){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	404 addComment("[WARNING] some genes selected by the input filter are not in the expression file",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	405 rowToKeep=intersect(rowToKeep,rownames(expressionMatrix))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	406 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	407
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	408 if(length(rowToKeep)==0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	409 addComment("[ERROR]No gene survived to the input filtering thresholds, execution will be aborted.
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	410 Please consider to change threshold values and re-run the tool.",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	411 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	412 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	413
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	414 #filter comparison matrix
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	415 if(!is.null(comparisonMatrix)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	416 comparisonMatrix=matrix(comparisonMatrix[rowToKeep,],ncol=ncol(comparisonMatrix),dimnames = list(rowToKeep,colnames(comparisonMatrix)))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	417 if(!is.null(comparisonMatrixInfoGene))comparisonMatrixInfoGene=comparisonMatrixInfoGene[rowToKeep]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	418 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	419 #then expression matrix
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	420 if(expressionToCluster)expressionMatrix=matrix(expressionMatrix[rowToKeep,],ncol=ncol(expressionMatrix),dimnames = list(rowToKeep,colnames(expressionMatrix)))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	421
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	422 if(!is.null(comparisonMatrix) && expressionToCluster && nrow(comparisonMatrix)!=nrow(expressionMatrix)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	423 addComment("[ERROR]Problem during input filtering, please check code",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	424 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	425 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	426
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	427 addComment("[INFO]Filtering step done",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	428 addComment(c("[INFO]Input filtering step:",length(rowToKeep),"remaining rows"),T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	429 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	430
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	431
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	432 addComment("[INFO]Ready to plot",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	433
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	434 ##---------------------
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	435
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	436 #plot heatmap
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	437 if(expressionToCluster){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	438 #will make clustering based on expression value or generic value
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	439 dataToHeatMap=expressionMatrix
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	440 valueMeaning="Intensity"
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	441 if(!is.null(opt$genericData))valueMeaning="Value"
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	442 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	443 #will make clustering on log2(FC) values
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	444 dataToHeatMap=matrix(comparisonMatrix[,seq(4,ncol(comparisonMatrix),nbColPerContrast)],ncol=nbComparisons,dimnames = list(rownames(comparisonMatrix),colnames(comparisonMatrix)[seq(1,ncol(comparisonMatrix),nbColPerContrast)]))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	445 valueMeaning="Log2(FC)"
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	446 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	447 addComment(c("[INFO]Dim of heatmap matrix:",dim(dataToHeatMap)),T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	448
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	449 if(nrow(dataToHeatMap)==1 && ncol(dataToHeatMap)==1){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	450 addComment("[ERROR]Cannot make clustering with unique cell tab",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	451 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	452 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	453
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	454
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	455 #apply data transformation if needed
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	456 if(opt$dataTransformation=="log"){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	457 dataToHeatMap=log(dataToHeatMap)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	458 valueMeaning=paste(c("log(",valueMeaning,")"),collapse="")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	459 addComment("[INFO]Data to cluster and to display in the heatmap are log transformed",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	460 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	461 if(opt$dataTransformation=="log2"){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	462 dataToHeatMap=log2(dataToHeatMap)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	463 valueMeaning=paste(c("log2(",valueMeaning,")"),collapse="")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	464 addComment("[INFO]Data to cluster and to display in the heatmap are log2 transformed",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	465 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	466
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	467 maxRowsToDisplay=opt$maxRows
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	468
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	469 nbClusters=opt$clusterNumber
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	470 if(nbClusters>nrow(dataToHeatMap)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	471 #correct number of clusters if needed
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	472 nbClusters=nrow(dataToHeatMap)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	473 addComment(c("[WARNING]Not enough rows to reach required clusters number, it is reduced to number of rows:",nbClusters),T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	474 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	475
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	476 nbSampleClusters=opt$sampleClusterNumber
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	477 if(nbSampleClusters>ncol(dataToHeatMap)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	478 #correct number of clusters if needed
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	479 nbSampleClusters=ncol(dataToHeatMap)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	480 addComment(c("[WARNING]Not enough columns to reach required conditions clusters number, it is reduced to number of columns:",nbSampleClusters),T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	481 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	482
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	483 colClust=FALSE
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	484 rowClust=FALSE
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	485 effectiveRowClust=FALSE
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	486
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	487 #make appropriate clustering if needed
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	488 if(nrow(dataToHeatMap)>1 && nbClusters>1)rowClust=hclust(distExtended(dataToHeatMap,method = opt$distanceMeasure),method = opt$aggloMethod)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	489 if(ncol(dataToHeatMap)>1 && nbSampleClusters>1)colClust=hclust(distExtended(t(dataToHeatMap),method = opt$distanceMeasure),method = opt$aggloMethod)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	490
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	491 if(nrow(dataToHeatMap)>maxRowsToDisplay){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	492 #make subsampling based on preliminary global clustering
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	493 #clusteringResults=cutree(rowClust,nbClusters)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	494 #heatMapGenesToKeep=unlist(lapply(seq(1,nbClusters),function(x)sample(which(clusteringResults==x),min(length(which(clusteringResults==x)),round(maxRowsToDisplay/nbClusters)))))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	495 ##OR
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	496 #basic subsampling
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	497 heatMapGenesToKeep=sample(rownames(dataToHeatMap),maxRowsToDisplay)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	498 effectiveDataToHeatMap=matrix(dataToHeatMap[heatMapGenesToKeep,],ncol=ncol(dataToHeatMap),dimnames=list(heatMapGenesToKeep,colnames(dataToHeatMap)))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	499 effectiveNbClusters=min(nbClusters,maxRowsToDisplay)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	500 if(nrow(effectiveDataToHeatMap)>1 && effectiveNbClusters>1)effectiveRowClust=hclust(distExtended(effectiveDataToHeatMap, method = opt$distanceMeasure),method = opt$aggloMethod)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	501 addComment(c("[WARNING]Too many rows for efficient heatmap drawing",maxRowsToDisplay,"subsampling is done for vizualization only"),T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	502 rm(heatMapGenesToKeep)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	503 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	504 effectiveDataToHeatMap=dataToHeatMap
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	505 effectiveRowClust=rowClust
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	506 effectiveNbClusters=nbClusters
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	507 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	508
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	509 addComment(c("[INFO]Dim of plotted heatmap matrix:",dim(effectiveDataToHeatMap)),T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	510
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	511 personalized_hoverinfo=matrix("",ncol = ncol(effectiveDataToHeatMap),nrow = nrow(effectiveDataToHeatMap),dimnames = dimnames(effectiveDataToHeatMap))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	512 if(expressionToCluster){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	513 for(iCol in colnames(effectiveDataToHeatMap)){for(iRow in rownames(effectiveDataToHeatMap)){personalized_hoverinfo[iRow,iCol]=paste(c("Probe: ",iRow,"\nCondition: ",iCol,"\n",valueMeaning,": ",effectiveDataToHeatMap[iRow,iCol]),collapse="")}}
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	514 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	515 for(iCol in colnames(effectiveDataToHeatMap)){for(iRow in rownames(effectiveDataToHeatMap)){personalized_hoverinfo[iRow,iCol]=paste(c("Probe: ",iRow,"\nCondition: ",iCol,"\nFC: ",round(2^effectiveDataToHeatMap[iRow,iCol],2)),collapse="")}}
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	516 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	517
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	518 #trying to overcome limitation of heatmaply package to modify xtick and ytick label, using directly plotly functions, but for now plotly do not permit to have personalized color for each x/y tick separately
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	519 test=FALSE
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	520 if(test==TRUE){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	521
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	522 #define dendogram shapes
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	523 dd.row <- as.dendrogram(effectiveRowClust)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	524 dd.col <- as.dendrogram(colClust)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	525
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	526 #and color them
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	527 dd.row=color_branches(dd.row, k = effectiveNbClusters, groupLabels = T)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	528 dd.col=color_branches(dd.col, k = nbSampleClusters, groupLabels = T)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	529
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	530 #generating function for dendogram from segment list
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	531 ggdend <- function(df) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	532 ggplot() +
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	533 geom_segment(data = df, aes(x=x, y=y, xend=xend, yend=yend)) +
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	534 labs(x = "", y = "") + theme_minimal() +
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	535 theme(axis.text = element_blank(), axis.ticks = element_blank(),
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	536 panel.grid = element_blank())
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	537 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	538
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	539 # generate x/y dendogram plots
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	540 px <- ggdend(dendro_data(dd.col)$segments)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	541 py <- ggdend(dendro_data(dd.row)$segments) + coord_flip()
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	542
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	543 # reshape data matrix
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	544 col.ord <- order.dendrogram(dd.col)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	545 row.ord <- order.dendrogram(dd.row)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	546 xx <- effectiveDataToHeatMap[row.ord, col.ord]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	547 # and also personalized_hoverinfo
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	548 personalized_hoverinfo=personalized_hoverinfo[row.ord, col.ord]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	549
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	550 # hide axis ticks and grid lines
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	551 eaxis <- list(
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	552 showticklabels = FALSE,
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	553 showgrid = FALSE,
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	554 zeroline = FALSE
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	555 )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	556
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	557 #make the empty plot
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	558 p_empty <- plot_ly() %>%
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	559 layout(margin = list(l = 200),
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	560 xaxis = eaxis,
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	561 yaxis = eaxis)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	562
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	563 heatmap.plotly <- plot_ly(
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	564 z = xx, x = 1:ncol(xx), y = 1:nrow(xx), colors = viridis(n = 101, alpha = 1, begin = 0, end = 1, option = "inferno"),
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	565 type = "heatmap", showlegend = FALSE, text = personalized_hoverinfo, hoverinfo = "text",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	566 colorbar = list(
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	567 # Capitalise first letter
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	568 title = valueMeaning,
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	569 tickmode = "array",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	570 len = 0.3
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	571 )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	572 ) %>%
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	573 layout(
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	574 xaxis = list(
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	575 tickfont = list(size = 10,color=get_leaves_branches_col(dd.row)),
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	576 tickangle = 45,
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	577 tickvals = 1:ncol(xx), ticktext = colnames(xx),
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	578 linecolor = "#ffffff",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	579 range = c(0.5, ncol(xx) + 0.5),
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	580 showticklabels = TRUE
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	581 ),
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	582 yaxis = list(
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	583 tickfont = list(size = 10, color=get_leaves_branches_col(dd.col)),
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	584 tickangle = 0,
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	585 tickvals = 1:nrow(xx), ticktext = rownames(xx),
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	586 linecolor = "#ffffff",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	587 range = c(0.5, nrow(xx) + 0.5),
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	588 showticklabels = TRUE
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	589 )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	590 )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	591
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	592 #generate plotly
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	593 pp <- subplot(px, p_empty, heatmap.plotly, py, nrows = 2, margin = 0,widths = c(0.8,0.2),heights = c(0.2,0.8), shareX = TRUE,
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	594 shareY = TRUE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	595
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	596 #save image file
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	597 export(pp, file = paste(c(file.path(getwd(), "plotDir"),"/Heatmap.",opt$format),collapse=""))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	598 #rise a bug due to token stuf
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	599 #orca(pp, file = paste(c(file.path(getwd(), "plotDir"),"/Heatmap.",opt$format),collapse=""))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	600
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	601
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	602 #save plotLy file
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	603 htmlwidgets::saveWidget(as_widget(pp), paste(c(file.path(getwd(), "plotLyDir"),"/Heatmap.html"),collapse=""),selfcontained = F)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	604
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	605 #htmlwidgets::saveWidget(as_widget(pp),"~/Bureau/test.html",selfcontained = F)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	606
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	607 }else{ #test
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	608 label_names=c("Probe","Condition",valueMeaning)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	609
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	610 # #color hclust objects
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	611 # dd.row=color_branches(effectiveRowClust, k = effectiveNbClusters)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	612 # #rowColors=get_leaves_branches_col(dd.row)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	613 # #rowColors[order.dendrogram(dd.row)]=rowColors
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	614 # rowGroup=cutree(effectiveRowClust, k = effectiveNbClusters)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	615 #
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	616 # #get order of class as they will be displayed on the dendogram
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	617 # rowGroupRenamed=data.frame(cluster=mapvalues(rowGroup, unique(rowGroup[order.dendrogram(dd.row)[nleaves(dd.row):1]]), 1:effectiveNbClusters))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	618 #
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	619 # dd.col=color_branches(colClust, k = nbSampleClusters)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	620 # #colColors=get_leaves_branches_col(dd.col)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	621 # #colColors[order.dendrogram(dd.col)]=colColors
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	622 # colGroup=cutree(colClust, k = nbSampleClusters)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	623 #
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	624 # # #get order of class as they will be displayed on the dendogram
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	625 # colGroupRenamed=data.frame(sampleCluster=mapvalues(colGroup, unique(colGroup[order.dendrogram(dd.col)[nleaves(dd.col):1]]), 1:nbSampleClusters))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	626
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	627
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	628 #while option is not correctly managed by heatmap apply, put personalized_hoverinfo to NULL
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	629 personalized_hoverinfo=NULL
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	630
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	631 if(is.null(opt$personalColors)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	632 heatmapColors=viridis(n = 101, alpha = 1, begin = 0, end = 1, option = "inferno")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	633 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	634 heatmapColors=personalColors
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	635 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	636
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	637 colGroupRenamed=NULL
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	638 if(!is.null(factorInfoMatrix)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	639 colGroupRenamed=eval(parse(text=(paste("data.frame(",factorBarColor,"=factorInfoMatrix[colnames(effectiveDataToHeatMap),2])",sep=""))))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	640 sideBarGroupNb=length(table(factorInfoMatrix[colnames(effectiveDataToHeatMap),2]))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	641 sideBarColorPaletteName="Spectral"
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	642 if(!is.null(opt$sideBarColorPalette) && opt$sideBarColorPalette%in%rownames(RColorBrewer::brewer.pal.info)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	643 sideBarColorPaletteName=opt$sideBarColorPalette
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	644 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	645 sideBarColorPalette=setNames(colorRampPalette(RColorBrewer::brewer.pal(RColorBrewer::brewer.pal.info[sideBarColorPaletteName,"maxcolors"], sideBarColorPaletteName))(sideBarGroupNb),unique(factorInfoMatrix[colnames(effectiveDataToHeatMap),2]))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	646 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	647
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	648 if(!is.null(colGroupRenamed)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	649 pp <- heatmaply(effectiveDataToHeatMap,key.title = valueMeaning,k_row=effectiveNbClusters,k_col=nbSampleClusters,col_side_colors=colGroupRenamed,col_side_palette=sideBarColorPalette,Rowv=effectiveRowClust,Colv=colClust,label_names=label_names,custom_hovertext=personalized_hoverinfo,plot_method = "plotly",colors = heatmapColors)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	650 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	651 pp <- heatmaply(effectiveDataToHeatMap,key.title = valueMeaning,k_row=effectiveNbClusters,k_col=nbSampleClusters,Rowv=effectiveRowClust,Colv=colClust,label_names=label_names,custom_hovertext=personalized_hoverinfo,plot_method = "plotly",colors = heatmapColors)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	652 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	653
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	654
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	655 #save image file
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	656 export(pp, file = paste(c(file.path(getwd(), "plotDir"),"/Heatmap.",opt$format),collapse=""))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	657 #rise a bug due to token stuf
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	658 #orca(pp, file = paste(c(file.path(getwd(), "plotDir"),"/Heatmap.",opt$format),collapse=""))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	659
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	660
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	661 #save plotLy file
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	662 htmlwidgets::saveWidget(as_widget(pp), paste(c(file.path(getwd(), "plotLyDir"),"/Heatmap.html"),collapse=""),selfcontained = F)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	663
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	664 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	665 addComment("[INFO]Heatmap drawn",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	666
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	667
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	668 #plot circular heatmap
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	669 if(!class(effectiveRowClust)=="logical"){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	670 dendo=as.dendrogram(effectiveRowClust)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	671
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	672 if(is.null(opt$personalColors)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	673 col_fun = colorRamp2(quantile(effectiveDataToHeatMap,probs = seq(0,1,0.01)), viridis(101,option = "inferno"))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	674 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	675 col_fun = colorRamp2(quantile(effectiveDataToHeatMap,probs = seq(0,1,0.5)), personalColors)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	676 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	677
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	678 if(opt$format=="pdf"){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	679 pdf(paste(c("./plotDir/circularPlot.pdf"),collapse=""))}else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	680 png(paste(c("./plotDir/circularPlot.png"),collapse=""))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	681 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	682
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	683 circos.par(cell.padding = c(0, 0, 0, 0), gap.degree = 5)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	684 circos.initialize(c(rep("a",nrow(effectiveDataToHeatMap)),"b"),xlim=cbind(c(0,0),c(nrow(effectiveDataToHeatMap),5)))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	685 circos.track(ylim = c(0, 1), bg.border = NA, panel.fun = function(x, y) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	686 if(CELL_META$sector.index=="a"){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	687 nr = ncol(effectiveDataToHeatMap)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	688 nc = nrow(effectiveDataToHeatMap)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	689 circos.text(1:nc- 0.5, rep(0,nc), adj = c(0, 0),
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	690 rownames(effectiveDataToHeatMap)[order.dendrogram(dendo)], facing = "clockwise", niceFacing = TRUE, cex = 0.3)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	691 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	692 })
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	693
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	694 circos.track(ylim = c(0, ncol(effectiveDataToHeatMap)), bg.border = NA, panel.fun = function(x, y) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	695
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	696 m = t(matrix(effectiveDataToHeatMap[order.dendrogram(dendo),],ncol=ncol(effectiveDataToHeatMap)))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	697 col_mat = col_fun(m)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	698 nr = nrow(m)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	699 nc = ncol(m)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	700 if(CELL_META$sector.index=="a"){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	701 for(i in 1:nr) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	702 circos.rect(1:nc - 1, rep(nr - i, nc),
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	703 1:nc, rep(nr - i + 1, nc),
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	704 border = col_mat[i, ], col = col_mat[i, ])
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	705 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	706 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	707 circos.text(rep(1,nr), seq(nr,1,-1) , colnames(effectiveDataToHeatMap),cex = 0.3)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	708 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	709 })
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	710
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	711 #dendo = color_branches(dendo, k = effectiveNbClusters, col = colorRampPalette(brewer.pal(12,"Set3"))(effectiveNbClusters))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	712 dendo = color_branches(dendo, k = effectiveNbClusters, col = rev(colorspace::rainbow_hcl(effectiveNbClusters)))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	713
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	714
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	715 circos.track(ylim = c(0, attributes(dendo)$height), bg.border = NA, track.height = 0.25,
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	716 panel.fun = function(x, y) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	717 if(CELL_META$sector.index=="a")circos.dendrogram(dendo)} )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	718
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	719 circos.clear()
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	720 ##add legend
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	721 lgd_links = Legend(at = seq(ceiling(min(effectiveDataToHeatMap)),floor(max(effectiveDataToHeatMap)),ceiling((floor(max(effectiveDataToHeatMap))-ceiling(min(effectiveDataToHeatMap)))/4)), col_fun = col_fun,
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	722 title_position = "topleft", grid_width = unit(5, "mm") ,title = valueMeaning)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	723
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	724 pushViewport(viewport(x = 0.85, y = 0.80,
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	725 width = 0.1,
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	726 height = 0.1,
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	727 just = c("left", "bottom")))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	728 grid.draw(lgd_links)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	729 upViewport()
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	730
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	731
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	732 dev.off()
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	733
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	734 addComment("[INFO]Circular heatmap drawn",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	735 loc <- Sys.setlocale("LC_NUMERIC","C")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	736 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	737 addComment(c("[WARNING]Circular plot will not be plotted considering row or cluster number < 2"),T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	738 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	739 rm(effectiveDataToHeatMap,effectiveRowClust,effectiveNbClusters)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	740
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	741 #plot screeplot
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	742 if(class(rowClust)!="logical" && nrow(dataToHeatMap)>2){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	743 screePlotData=c()
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	744 for(iNbClusters in 2:(nbClusters+min(10,max(0,nrow(dataToHeatMap)-nbClusters)))){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	745 clusteringResults=cutree(rowClust,iNbClusters)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	746 #clusteringResults=kmeans(dataToHeatMap,iNbClusters)$cluster
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	747
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	748 #compute variance between each intra-class points amongst themselves (need at least 3 points by cluster)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	749 #screePlotData=c(screePlotData,sum(unlist(lapply(seq(1,iNbClusters),function(x){temp=which(clusteringResults==x);if(length(temp)>2){var(dist(dataToHeatMap[temp,]))}else{0}}))) )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	750 #compute variance between each intra-class points and fictive mean point (need at least 2 points by cluster)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	751 #screePlotData=c(screePlotData,sum(unlist(lapply(seq(1,iNbClusters),function(x){temp=which(clusteringResults==x);if(length(temp)>1){ var(dist(rbind(apply(dataToHeatMap[temp,],2,mean),dataToHeatMap[temp,]))[1:length(temp)]) }else{0}}))) )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	752 if(ncol(dataToHeatMap)>1)screePlotData=c(screePlotData,sum(unlist(lapply(seq(1,iNbClusters),function(x){temp=which(clusteringResults==x);if(length(temp)>1){ sum((distExtended(rbind(apply(dataToHeatMap[temp,],2,mean),dataToHeatMap[temp,]),method = opt$distanceMeasure)[1:length(temp)])^2) }else{0}}))) )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	753 else screePlotData=c(screePlotData,sum(unlist(lapply(seq(1,iNbClusters),function(x){temp=which(clusteringResults==x);if(length(temp)>1){ sum((dataToHeatMap[temp,]-mean(dataToHeatMap[temp,]))^2) }else{0}}))) )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	754 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	755
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	756 dataToPlot=data.frame(clusterNb=seq(2,length(screePlotData)+1),wcss=screePlotData)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	757 p <- ggplot(data=dataToPlot, aes(clusterNb,wcss)) + geom_point(colour="#EE4444") + geom_line(colour="#DD9999") +
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	758 ggtitle("Scree plot") + theme_bw() + xlab(label="Cluster number") + ylab(label="Within cluster sum of squares") +
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	759 theme(panel.border=element_blank(),plot.title = element_text(hjust = 0.5),legend.position = "none") +
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	760 scale_x_continuous(breaks=seq(min(dataToPlot$clusterNb), max(dataToPlot$clusterNb), 1))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	761
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	762 #save plotly files
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	763 pp <- ggplotly(p)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	764
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	765 if(opt$format=="pdf"){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	766 pdf(paste(c("./plotDir/screePlot.pdf"),collapse=""))}else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	767 png(paste(c("./plotDir/screePlot.png"),collapse=""))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	768 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	769 plot(p)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	770 dev.off()
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	771
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	772 #save plotly files
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	773 htmlwidgets::saveWidget(as_widget(pp), paste(c(file.path(getwd(), "plotLyDir"),"/screePlot.html"),collapse=""),selfcontained = F)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	774
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	775 addComment("[INFO]Scree plot drawn",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	776 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	777 addComment(c("[WARNING]Scree plot will not be plotted considering row number <= 2"),T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	778 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	779
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	780 ##----------------------
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	781
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	782 #filter output based on parameters
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	783
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	784 rowToKeep=rownames(dataToHeatMap)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	785 if(!is.null(opt$filterInputOutput) && opt$filterInputOutput=="output"){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	786 #rowToKeep=intersect(which(comparisonMatrix[,seq(2,ncol(comparisonMatrix),4)]<=opt$pvalThreshold),which(abs(comparisonMatrix[,seq(4,ncol(comparisonMatrix),4)])>=log2(opt$FCthreshold)))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	787 if(is.null(opt$geneListFiltering)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	788 if(is.null(opt$genericData)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	789 #diff. expression matrix
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	790 rowToKeep=names(which(unlist(apply(comparisonMatrix,1,function(x)length(intersect(which(x[seq(2,length(x),nbColPerContrast)]<=opt$pvalThreshold),which(abs(x[seq(4,length(x),nbColPerContrast)])>=log2(opt$FCthreshold))))!=0))))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	791 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	792 #generic filtering matrix
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	793 rowToKeep=rownames(comparisonMatrix)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	794 if(!is.null(opt$comparisonNameLow)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	795 restrictedLowComparisons=unlist(strsplit(opt$comparisonNameLow,","))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	796 rowToKeep=intersect(rowToKeep,names(which(unlist(apply(comparisonMatrix,1,function(x)length(which(x[restrictedLowComparisons]>opt$FCthreshold))!=0)))))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	797 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	798 if(!is.null(opt$comparisonNameHigh)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	799 restrictedHighComparisons=unlist(strsplit(opt$comparisonNameHigh,","))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	800 rowToKeep=intersect(rowToKeep,names(which(unlist(apply(comparisonMatrix,1,function(x)length(which(x[restrictedHighComparisons]<opt$pvalThreshold))!=0)))))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	801 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	802 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	803 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	804 geneListFiltering=read.csv(opt$geneListFiltering,as.is = 1,header=F)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	805 rowToKeep=unlist(c(geneListFiltering))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	806 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	807 if(!is.null(comparisonMatrix) && !all(rowToKeep%in%rownames(comparisonMatrix))){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	808 #should arrive only with user gene list filtering with diff.exp. results clustering
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	809 addComment("[WARNING] some genes of the user defined list are not in the diff. exp. input file",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	810 rowToKeep=intersect(rowToKeep,rownames(comparisonMatrix))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	811 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	812
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	813 if(expressionToCluster && !all(rowToKeep%in%rownames(expressionMatrix))){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	814 addComment("[WARNING] some genes selected by the output filter are not in the expression file",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	815 rowToKeep=intersect(rowToKeep,rownames(expressionMatrix))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	816 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	817 addComment(c("[INFO]Output filtering step:",length(rowToKeep),"remaining rows"),T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	818 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	819
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	820 #we add differential analysis info in output if it was directly used for clustering or when it was used for filtering with expression
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	821
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	822 #in case of expression or generic data clustering without filtering based on external stats
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	823 if(expressionToCluster && is.null(comparisonMatrix)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	824 if(length(rowToKeep)==0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	825 addComment("[WARNING]No more gene after output filtering step, tabular output will be empty",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	826 outputData=matrix(c("Gene","Cluster","noGene","noClustering"),ncol=2,nrow=2,byrow = TRUE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	827 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	828 outputData=matrix(0,ncol=2,nrow=length(rowToKeep)+1)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	829 outputData[1,]=c("Gene","Cluster")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	830 outputData[2:(length(rowToKeep)+1),1]=rowToKeep
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	831 if(class(rowClust)!="logical" ){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	832 outputData[2:(length(rowToKeep)+1),2]=cutree(rowClust,nbClusters)[rowToKeep]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	833 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	834 outputData[2:(length(rowToKeep)+1),2]=0
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	835 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	836 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	837 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	838
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	839 #in case of generic data clustering with filtering based on generic external data
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	840 if(!is.null(opt$genericData) && !is.null(comparisonMatrix)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	841 if(length(rowToKeep)==0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	842 addComment("[WARNING]No more gene after output filtering step, tabular output will be empty",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	843 outputData=matrix(c("Gene","Cluster","noGene","noClustering"),ncol=2,nrow=2,byrow = TRUE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	844 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	845 outputData=matrix(0,ncol=2+nbComparisons,nrow=length(rowToKeep)+1)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	846 outputData[1,]=c("Gene","Cluster",colnames(comparisonMatrix))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	847 outputData[2:(length(rowToKeep)+1),1]=rowToKeep
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	848 if(class(rowClust)!="logical" ){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	849 outputData[2:(length(rowToKeep)+1),2]=cutree(rowClust,nbClusters)[rowToKeep]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	850 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	851 outputData[2:(length(rowToKeep)+1),2]=0
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	852 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	853 outputData[2:(length(rowToKeep)+1),3:(ncol(comparisonMatrix)+2)]=prettyNum(comparisonMatrix[rowToKeep,],digits=4)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	854 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	855 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	856
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	857 #in case of expression data clustering with filtering based on diff. exp. results or diff. exp. results clustering
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	858 if(is.null(opt$genericData) && !is.null(comparisonMatrix)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	859 if(length(rowToKeep)==0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	860 addComment("[WARNING]No more gene after output filtering step, tabular output will be empty",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	861 outputData=matrix(0,ncol=3,nrow=3)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	862 outputData[1,]=c("","","Comparison")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	863 outputData[2,]=c("Gene","Info","Cluster")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	864 outputData[3,]=c("noGene","noInfo","noClustering")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	865 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	866 outputData=matrix(0,ncol=3+nbComparisons*nbColPerContrast,nrow=length(rowToKeep)+2)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	867 outputData[1,]=c("","","Comparison",rep(colnames(comparisonMatrix)[seq(1,ncol(comparisonMatrix),nbColPerContrast)],each=nbColPerContrast))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	868 outputData[2,]=c("Gene","Info","Cluster",rep(c("p-val","FDR.p-val","FC","log2(FC)","t-stat"),nbComparisons))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	869 outputData[3:(length(rowToKeep)+2),1]=rowToKeep
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	870 outputData[3:(length(rowToKeep)+2),2]=comparisonMatrixInfoGene[rowToKeep]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	871 if(class(rowClust)!="logical" ){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	872 outputData[3:(length(rowToKeep)+2),3]=cutree(rowClust,nbClusters)[rowToKeep]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	873 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	874 outputData[3:(length(rowToKeep)+2),3]=0
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	875 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	876 outputData[3:(length(rowToKeep)+2),4:(ncol(comparisonMatrix)+3)]=prettyNum(comparisonMatrix[rowToKeep,],digits=4)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	877 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	878 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	879
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	880 addComment("[INFO]Formated output",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	881 write.table(outputData,file=opt$outputFile,quote=FALSE,sep="\t",col.names = F,row.names = F)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	882
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	883 ##----------------------
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	884
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	885 end.time <- Sys.time()
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	886 addComment(c("[INFO]Total execution time for R script:",as.numeric(end.time - start.time,units="mins"),"mins"),T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	887
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	888
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	889 addComment("[INFO]End of R script",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	890
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	891 printSessionInfo(opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	892
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	893 #sessionInfo()
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	894
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	895
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	896

Mercurial > repos > vandelj > giant_limma_analysis

annotate src/heatMapClustering.R @ 0:f274c8d45613 draft