giant_volcano_plot: src/ExprPlotsScript.R annotate

annotate src/ExprPlotsScript.R @ 0:c9a38c1eadf1 draft

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

author	vandelj
date	Fri, 26 Jun 2020 09:45:41 -0400
parents
children

rev	line source
0 c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	1 # A command-line interface to basic plots for use with Galaxy
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	2 # written by Jimmy Vandel
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	3 # one of these arguments is required:
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	4 #
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	5 #
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	6 initial.options <- commandArgs(trailingOnly = FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	7 file.arg.name <- "--file="
c9a38c1eadf1 "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)])
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	9 script.basename <- dirname(script.name)
c9a38c1eadf1 "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"))
c9a38c1eadf1 "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"))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	12
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	13 #addComment("Welcome R!")
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	14
c9a38c1eadf1 "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
c9a38c1eadf1 "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 ) } )
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	17
c9a38c1eadf1 "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.
c9a38c1eadf1 "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")
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	20 loc <- Sys.setlocale("LC_NUMERIC", "C")
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	21
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	22 #get starting time
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	23 start.time <- Sys.time()
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	24
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	25 #get options
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	26 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	27 args <- commandArgs()
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	28
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	29
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	30 # get options, using the spec as defined by the enclosed list.
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	31 # we read the options from the default: commandArgs(TRUE).
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	32 spec <- matrix(c(
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	33 "dataFile", "i", 1, "character",
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	34 "factorInfo","t", 1, "character",
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	35 "dataFileFormat","j",1,"character",
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	36 "conditionNames","c",1,"character",
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	37 "format", "f", 1, "character",
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	38 "quiet", "q", 0, "logical",
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	39 "log", "l", 1, "character",
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	40 "histo" , "h", 1, "character",
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	41 "maPlot" , "a", 1, "character",
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	42 "boxplot" , "b", 1, "character",
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	43 "microarray" , "m", 1, "character",
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	44 "acp" , "p" , 1, "character",
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	45 "screePlot" , "s" , 1, "character"),
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	46 byrow=TRUE, ncol=4)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	47 opt <- getopt(spec)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	48
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	49 # enforce the following required arguments
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	50 if (is.null(opt$log)) {
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	51 addComment("[ERROR]'log file' is required")
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	52 q( "no", 1, F )
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	53 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	54 addComment("[INFO]Start of R script",T,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	55 if (is.null(opt$dataFile) \|\| is.null(opt$dataFileFormat)) {
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	56 addComment("[ERROR]'dataFile' and it format are required",T,opt$log)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	57 q( "no", 1, F )
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	58 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	59 if (is.null(opt$format)) {
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	60 addComment("[ERROR]'output format' is required",T,opt$log)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	61 q( "no", 1, F )
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	62 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	63 if (is.null(opt$histo) & is.null(opt$maPlot) & is.null(opt$boxplot) & is.null(opt$microarray) & is.null(opt$acp)){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	64 addComment("[ERROR]Select at least one plot to draw",T,opt$log)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	65 q( "no", 1, F )
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	66 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	67
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	68 verbose <- if (is.null(opt$quiet)) {
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	69 TRUE
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	70 }else{
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	71 FALSE}
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	72
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	73 addComment("[INFO]Parameters checked!",T,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	74
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	75 addComment(c("[INFO]Working directory: ",getwd()),TRUE,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	76 addComment(c("[INFO]Command line: ",args),TRUE,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	77
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	78 #directory for plots
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	79 dir.create(file.path(getwd(), "plotDir"))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	80 dir.create(file.path(getwd(), "plotLyDir"))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	81
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	82 #silent package loading
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	83 suppressPackageStartupMessages({
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	84 library("oligo")
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	85 library("ff")
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	86 library("ggplot2")
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	87 library("plotly")
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	88 })
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	89
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	90
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	91 #chargement des fichiers en entrée
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	92 #fichier de type CEL
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	93 dataAreFromCel=FALSE
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	94 if(toupper(opt$dataFileFormat)=="CEL"){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	95 dataAreFromCel=TRUE
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	96 celData=read.celfiles(unlist(strsplit(opt$dataFile,",")))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	97 #load all expressions
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	98 dataMatrix=exprs(celData)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	99 #select "pm" probes
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	100 probeInfo=getProbeInfo(celData,probeType = c("pm"),target="probeset")
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	101 #reduce dataMatrix to log expression matrix for a randomly probe selection
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	102 dataMatrix=log2(dataMatrix[sample(unique(probeInfo[,1]),min(100000,length(unique(probeInfo[,1])))),])
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	103 addComment("[INFO]Raw data are log2 transformed",TRUE,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	104 remove(probeInfo)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	105 }else{
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	106 #fichier deja tabule
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	107 dataMatrix=read.csv(file=opt$dataFile,header=F,sep="\t",colClasses="character")
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	108 #remove first row to convert it as colnames (to avoid X before colnames with header=T)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	109 colNamesData=dataMatrix[1,-1]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	110 dataMatrix=dataMatrix[-1,]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	111 #remove first colum to convert it as rownames
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	112 rowNamesData=dataMatrix[,1]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	113 dataMatrix=dataMatrix[,-1]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	114 if(is.data.frame(dataMatrix)){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	115 dataMatrix=data.matrix(dataMatrix)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	116 }else{
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	117 dataMatrix=data.matrix(as.numeric(dataMatrix))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	118 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	119 dimnames(dataMatrix)=list(rowNamesData,colNamesData)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	120 if(any(duplicated(rowNamesData)))addComment("[WARNING] several rows share the same probe/gene name, you should merge or rename them to avoid further analysis mistakes",TRUE,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	121 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	122
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	123 addComment("[INFO]Input data loaded",TRUE,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	124 addComment(c("[INFO]Dim of data matrix:",dim(dataMatrix)),T,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	125
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	126 #get number of conditions
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	127 nbConditions=ncol(dataMatrix)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	128
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	129 #get condition names if they are specified
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	130 if(!is.null(opt$conditionNames) && length(opt$conditionNames)==nbConditions){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	131 nameConditions=opt$conditionNames
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	132 colnames(dataMatrix)=nameConditions
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	133 #rownames(phenoData(celData)@data)=nameConditions
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	134 #rownames(protocolData(celData)@data)=nameConditions
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	135 }else{
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	136 nameConditions=colnames(dataMatrix)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	137 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	138
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	139 #create a correspondance table between plot file names and name displayed in figure legend and html items
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	140 correspondanceNameTable=matrix("",ncol=2,nrow=nbConditions)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	141 correspondanceNameTable[,1]=paste("Condition",1:nbConditions,sep="")
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	142 correspondanceNameTable[,2]=nameConditions
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	143 rownames(correspondanceNameTable)=correspondanceNameTable[,2]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	144
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	145 addComment("[INFO]Retreive condition names",TRUE,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	146
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	147 if(!is.null(opt$factorInfo)){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	148 #chargement du fichier des facteurs
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	149 factorInfoMatrix=read.csv(file=file.path(getwd(), opt$factorInfo),header=F,sep="\t",colClasses="character")
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	150 #remove first row to convert it as colnames
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	151 colnames(factorInfoMatrix)=factorInfoMatrix[1,]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	152 factorInfoMatrix=factorInfoMatrix[-1,]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	153 #use first colum to convert it as rownames but not removing it to avoid conversion as vector in unique factor case
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	154 rownames(factorInfoMatrix)=factorInfoMatrix[,1]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	155
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	156
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	157 if(length(setdiff(colnames(dataMatrix),rownames(factorInfoMatrix)))!=0){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	158 addComment("[ERROR]Missing samples in factor file",T,opt$log)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	159 q( "no", 1, F )
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	160 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	161
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	162 #order sample as in expression matrix and remove spurious sample
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	163 factorInfoMatrix=factorInfoMatrix[colnames(dataMatrix),]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	164
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	165 addComment("[INFO]Factors OK",T,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	166 addComment(c("[INFO]Dim of factorInfo matrix:",dim(factorInfoMatrix)),T,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	167
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	168 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	169
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	170 addComment("[INFO]Ready to plot",T,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	171
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	172
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	173 ##----------------------
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	174
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	175 ###plot histograms###
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	176 histogramPerFigure=50
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	177 if (!is.null(opt$histo)) {
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	178 for(iToPlot in 1:(((nbConditions-1)%/%histogramPerFigure)+1)){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	179 firstPlot=1+histogramPerFigure*(iToPlot-1)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	180 lastPlot=min(nbConditions,histogramPerFigure*iToPlot)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	181 dataToPlot=data.frame(x=c(dataMatrix[,firstPlot:lastPlot]),Experiment=rep(colnames(dataMatrix)[firstPlot:lastPlot],each=nrow(dataMatrix)))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	182 p <- ggplot(data=dataToPlot, aes(x = x, color=Experiment)) + stat_density(geom="line", size=1, position="identity") +
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	183 ggtitle("Intensity densities") + theme_bw() + ylab(label="Density") +
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	184 theme(panel.border=element_blank(),plot.title = element_text(hjust = 0.5))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	185 if(dataAreFromCel){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	186 #original ploting function
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	187 #hist(celData[,firstPlot:lastPlot],lty=rep(1,nbConditions)[firstPlot:lastPlot],lwd=2,which='pm',target="probeset",transfo=log2,col=rainbow(nbConditions)[firstPlot:lastPlot])
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	188 p <- p + xlab(label="Log2 intensities")
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	189 }else{
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	190 p <- p + xlab(label="Intensities")
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	191 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	192 if(opt$format=="pdf"){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	193 pdf(paste(c("./plotDir/",opt$histo,iToPlot,".pdf"),collapse=""))}else{
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	194 png(paste(c("./plotDir/",opt$histo,iToPlot,".png"),collapse=""))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	195 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	196 print(p)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	197 dev.off()
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	198 #save plotly files
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	199 pp <- ggplotly(p)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	200 htmlwidgets::saveWidget(as_widget(pp), paste(c(file.path(getwd(), "plotLyDir"),"/",opt$histo,iToPlot,".html"),collapse=""),selfcontained = F)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	201 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	202 remove(p,dataToPlot)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	203 addComment("[INFO]Histograms drawn",T,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	204 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	205
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	206 ##----------------------
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	207
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	208 ###plot MAplots###
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	209 MAplotPerPage=4
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	210 if (!is.null(opt$maPlot)) {
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	211 iToPlot=1
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	212 plotVector=list()
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	213 toTake=sample(nrow(dataMatrix),min(200000,nrow(dataMatrix)))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	214 refMedianColumn=rowMedians(as.matrix(dataMatrix[toTake,]))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	215 if(length(toTake)>100000)addComment(c("[INFO]high number of input data rows ",length(toTake),"; the generation of MA plot can take a while, please be patient"),TRUE,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	216 for (iCondition in 1:nbConditions){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	217 #MAplot(celData,which=i,what=pm,transfo=log2)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	218 #smoothScatter(x=xToPlot,y=yToPlot,main=nameConditions[iCondition])
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	219 dataA=dataMatrix[toTake,iCondition]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	220 dataB=refMedianColumn####ATTENTION PAR DEFAUT
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	221 xToPlot=0.5*(dataA+dataB)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	222 yToPlot=dataA-dataB
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	223 tempX=seq(min(xToPlot),max(xToPlot),0.1)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	224 tempY=unlist(lapply(tempX,function(x){median(yToPlot[intersect(which(xToPlot>=(x-0.1/2)),which(xToPlot<(x+0.1/2)))])}))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	225
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	226 dataToPlot=data.frame(x=xToPlot,y=yToPlot)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	227 dataMedianToPlot=data.frame(x=tempX,y=tempY)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	228 p <- ggplot(data=dataToPlot, aes(x,y)) + stat_density2d(aes(fill = ..density..^0.25), geom = "tile", contour = FALSE, n = 100) +
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	229 scale_fill_continuous(low = "white", high = "dodgerblue4") + geom_smooth(data=dataMedianToPlot,colour="red", size=0.5, se=FALSE) +
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	230 ggtitle(correspondanceNameTable[iCondition,2]) + theme_bw() + xlab(label="") + ylab(label="") +
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	231 theme(panel.border=element_blank(),plot.title = element_text(hjust = 0.5),legend.position = "none")
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	232 plotVector[[length(plotVector)+1]]=p
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	233
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	234 #save plotly files
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	235 pp <- ggplotly(p)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	236 htmlwidgets::saveWidget(as_widget(pp), paste(c(file.path(getwd(), "plotLyDir"),"/",opt$maPlot,"_",correspondanceNameTable[iCondition,1],".html"),collapse=""),selfcontained = F)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	237
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	238 if(iCondition==nbConditions \|\| length(plotVector)==MAplotPerPage){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	239 #define a new plotting file
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	240 if(opt$format=="pdf"){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	241 pdf(paste(c("./plotDir/",opt$maPlot,iToPlot,".pdf"),collapse=""))}else{
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	242 png(paste(c("./plotDir/",opt$maPlot,iToPlot,".png"),collapse=""))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	243 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	244 multiplot(plotlist=plotVector,cols=2)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	245 dev.off()
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	246 if(iCondition<nbConditions){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	247 #prepare for a new plotting file if necessary
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	248 plotVector=list()
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	249 iToPlot=iToPlot+1
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	250 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	251 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	252 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	253 remove(p,dataToPlot,dataA,dataB,toTake,xToPlot,yToPlot)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	254 addComment("[INFO]MAplots drawn",T,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	255 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	256
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	257 ##----------------------
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	258
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	259 ###plot boxplots###
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	260 boxplotPerFigure=50
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	261 if (!is.null(opt$boxplot)) {
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	262 for(iToPlot in 1:(((nbConditions-1)%/%boxplotPerFigure)+1)){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	263 firstPlot=1+boxplotPerFigure*(iToPlot-1)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	264 lastPlot=min(nbConditions,boxplotPerFigure*iToPlot)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	265 dataToPlot=data.frame(intensities=c(dataMatrix[,firstPlot:lastPlot]),Experiment=rep(colnames(dataMatrix)[firstPlot:lastPlot],each=nrow(dataMatrix)))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	266 #to make HTML file lighter, sampling will be done amongst outliers
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	267 #get outliers for each boxplot
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	268 boxplotsOutliers=apply(dataMatrix[,firstPlot:lastPlot],2,function(x)boxplot.stats(x)$out)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	269 #sample amongst them to keep at maximum of 1000 points and include both min and max outliers values
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	270 boxplotsOutliers=lapply(boxplotsOutliers,function(x)if(length(x)>0)c(sample(c(x),min(length(x),1000)),max(c(x)),min(c(x))))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	271 dataOutliers=data.frame(yVal=unlist(boxplotsOutliers),xVal=unlist(lapply(seq_along(boxplotsOutliers),function(x)rep(names(boxplotsOutliers)[x],length(boxplotsOutliers[[x]])))))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	272 #plot boxplots without outliers
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	273 p <- ggplot(data=dataToPlot, aes(y = intensities, x=Experiment ,color=Experiment)) + geom_boxplot(outlier.colour=NA,outlier.shape =NA) +
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	274 ggtitle("Intensities") + theme_bw() + xlab(label="") +
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	275 theme(panel.border=element_blank(),plot.title = element_text(hjust = 0.5),axis.text.x = element_text(angle = 45, hjust = 1),plot.margin=unit(c(10,10,max(unlist(lapply(dataToPlot$Experiment,function(x)nchar(as.character(x))))),15+max(unlist(lapply(dataToPlot$Experiment,function(x)nchar(as.character(x)))))),"mm"))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	276 #add to plot sampled outliers
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	277 p <- p + geom_point(data=dataOutliers,aes(x=xVal,y=yVal,color=xVal),inherit.aes = F)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	278 if(dataAreFromCel){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	279 #original plotting function
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	280 #boxplot(celData[,firstPlot:lastPlot],which='pm',col=rainbow(nbConditions)[firstPlot:lastPlot],target="probeset",transfo=log2,names=nameConditions[firstPlot:lastPlot],main="Intensities")
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	281 p <- p + ylab(label="Log2 intensities")
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	282 }else{
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	283 p <- p + ylab(label="Intensities")
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	284 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	285 if(opt$format=="pdf"){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	286 pdf(paste(c("./plotDir/",opt$boxplot,iToPlot,".pdf"),collapse=""))}else{
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	287 png(paste(c("./plotDir/",opt$boxplot,iToPlot,".png"),collapse=""))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	288 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	289 print(p)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	290 dev.off()
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	291 #save plotly files
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	292 pp <- ggplotly(p)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	293
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	294 #modify plotly object to get HTML file not too heavy for loading
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	295 for(iData in 1:length(pp$x$data)){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	296 ##get kept outliers y values
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	297 #yPointsToKeep=dataOutliers$yVal[which(dataOutliers$xVal==pp$x$data[[iData]]$name)]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	298 if(pp$x$data[[iData]]$type=="scatter"){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	299 ##scatter plot represent outliers points added to boxplot through geom_point
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	300 ##nothing to do as outliers have been sampled allready, just have to modify hover text
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	301 #if(length(yPointsToKeep)>0){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	302 #pointsToKeep=which(pp$x$data[[iData]]$y %in% yPointsToKeep)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	303 #pp$x$data[[iData]]$x=pp$x$data[[iData]]$x[pointsToKeep]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	304 #pp$x$data[[iData]]$y=pp$x$data[[iData]]$y[pointsToKeep]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	305 #pp$x$data[[iData]]$text=pp$x$data[[iData]]$text[pointsToKeep]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	306 #}else{
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	307 #pp$x$data[[iData]]$x=NULL
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	308 #pp$x$data[[iData]]$y=NULL
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	309 #pp$x$data[[iData]]$marker$opacity=0
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	310 #pp$x$data[[iData]]$hoverinfo=NULL
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	311 #pp$x$data[[iData]]$text=NULL
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	312 #}
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	313 #modify text to display
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	314 if(dataAreFromCel){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	315 pp$x$data[[iData]]$text=unlist(lapply(seq_along(pp$x$data[[iData]]$y),function(x)return(paste(c("log2(intensity) ",prettyNum(pp$x$data[[iData]]$y[x],digits=4)),collapse = ""))))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	316 }else{
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	317 pp$x$data[[iData]]$text=unlist(lapply(seq_along(pp$x$data[[iData]]$y),function(x)return(paste(c("intensity ",prettyNum(pp$x$data[[iData]]$y[x],digits=4)),collapse = ""))))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	318 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	319 }else{
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	320 ##disable marker plotting to keep only box and whiskers plot (outliers are displayed through scatter plot)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	321 pp$x$data[[iData]]$marker$opacity=0
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	322
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	323 #sample 50000 points amongst all data to get a lighter html file, sampling size should not be too low to avoid modifying limit of boxplots
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	324 pp$x$data[[iData]]$y=c(sample(dataMatrix[,pp$x$data[[iData]]$name],min(length(dataMatrix[,pp$x$data[[iData]]$name]),50000)),min(dataMatrix[,pp$x$data[[iData]]$name]),max(dataMatrix[,pp$x$data[[iData]]$name]))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	325 pp$x$data[[iData]]$x=rep(pp$x$data[[iData]]$x[1],length(pp$x$data[[iData]]$y))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	326
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	327 ##first remove outliers info
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	328 #downUpValues=boxplot.stats(dataMatrix[,pp$x$data[[iData]]$name])$stats
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	329 #if(verbose)addComment(c("filter values for boxplot",pp$x$data[[iData]]$name,"between",min(downUpValues),"and",max(downUpValues)),T,opt$log)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	330 #pointsToRemove=which(pp$x$data[[iData]]$y<min(downUpValues))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	331 #if(length(pointsToRemove)>0)pp$x$data[[iData]]$y=pp$x$data[[iData]]$y[-pointsToRemove]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	332 #pointsToRemove=which(pp$x$data[[iData]]$y>max(downUpValues))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	333 #if(length(pointsToRemove)>0)pp$x$data[[iData]]$y=pp$x$data[[iData]]$y[-pointsToRemove]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	334 #then add sampled outliers info
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	335 #pp$x$data[[iData]]$y=c(yPointsToKeep,pp$x$data[[iData]]$y)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	336 #pp$x$data[[iData]]$x=rep(pp$x$data[[iData]]$x[1],length(pp$x$data[[iData]]$y))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	337 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	338 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	339
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	340 htmlwidgets::saveWidget(as_widget(pp), paste(c(file.path(getwd(), "plotLyDir"),"/",opt$boxplot,iToPlot,".html"),collapse=""),selfcontained = F)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	341 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	342 remove(p,dataToPlot)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	343 addComment("[INFO]Boxplots drawn",T,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	344
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	345 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	346
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	347 ##----------------------
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	348
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	349 ###plot microarrays (only for .CEL files)###
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	350 if (!is.null(opt$microarray) && dataAreFromCel) {
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	351 for (iCondition in 1:nbConditions){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	352 if(opt$format=="pdf"){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	353 pdf(paste(c("./plotDir/",opt$microarray,"_",correspondanceNameTable[iCondition,1],".pdf"),collapse=""),onefile = F,width = 5,height = 5)}else{
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	354 png(paste(c("./plotDir/",opt$microarray,"_",correspondanceNameTable[iCondition,1],".png"),collapse=""))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	355 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	356 image(celData[,iCondition],main=correspondanceNameTable[iCondition,2])
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	357 dev.off()
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	358 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	359 addComment("[INFO]Microarray drawn",T,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	360 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	361
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	362 ##----------------------
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	363
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	364 ###plot PCA plot###
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	365 if (!is.null(opt$acp)){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	366 ##to avoid error when nrow is too large, results quite stable with 200k random selected rows
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	367 randomSelection=sample(nrow(dataMatrix),min(200000,nrow(dataMatrix)))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	368 #remove constant variables
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	369
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	370 dataFiltered=dataMatrix[randomSelection,]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	371 toRemove=which(unlist(apply(dataFiltered,1,var))==0)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	372 if(length(toRemove)>0){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	373 dataFiltered=dataFiltered[-toRemove,]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	374 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	375 ##geom_text(aes(label=Experiments,hjust=1, vjust=1.3), y = PC2+0.01)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	376 PACres = prcomp(t(dataFiltered),scale.=TRUE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	377
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	378 if(!is.null(opt$screePlot)){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	379 #scree plot
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	380 #p <- fviz_eig(PACres)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	381 dataToPlot=data.frame(compo=seq(1,length(PACres$sdev)),var=(PACres$sdev^2/sum(PACres$sdev^2))*100)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	382 p<-ggplot(data=dataToPlot, aes(x=compo, y=var)) + geom_bar(stat="identity", fill="steelblue") + geom_line() + geom_point() +
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	383 ggtitle("Scree plot") + theme_bw() + theme(panel.border=element_blank(),plot.title = element_text(hjust = 0.5)) +
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	384 xlab(label="Dimensions") + ylab(label="% explained variances") + scale_x_discrete(limits=dataToPlot$compo)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	385 pp <- ggplotly(p)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	386
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	387 if(opt$format=="pdf"){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	388 pdf(paste(c("./plotDir/",opt$screePlot,".pdf"),collapse=""))}else{
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	389 png(paste(c("./plotDir/",opt$screePlot,".png"),collapse=""))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	390 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	391 plot(p)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	392 dev.off()
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	393 htmlwidgets::saveWidget(as_widget(pp), paste(c(file.path(getwd(), "plotLyDir"),"/",opt$screePlot,".html"),collapse=""),selfcontained = F)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	394 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	395
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	396 #now plot pca plots
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	397
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	398 if(!is.null(opt$factorInfo)){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	399 fileIdent=""
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	400 symbolset = c("circle","cross","square","diamond","circle-open","square-open","diamond-open","x")
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	401
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	402 #save equivalence between real factor names and generic ones in correspondanceNameTable
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	403 correspondanceNameTable=rbind(correspondanceNameTable,matrix(c(paste("Factor",1:(ncol(factorInfoMatrix)-1),sep=""),colnames(factorInfoMatrix)[-1]),ncol=2,nrow=ncol(factorInfoMatrix)-1))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	404 rownames(correspondanceNameTable)=correspondanceNameTable[,2]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	405
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	406 #first order factors from decreasing groups number
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	407 orderedFactors=colnames(factorInfoMatrix)[-1][order(unlist(lapply(colnames(factorInfoMatrix)[-1],function(x)length(table(factorInfoMatrix[,x])))),decreasing = T)]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	408 allFactorsBigger=length(table(factorInfoMatrix[,orderedFactors[length(orderedFactors)]]))>length(symbolset)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	409 if(allFactorsBigger)addComment("[WARNING]All factors are composed of too many groups to display two factors at same time, each PCA plot will display only one factor groups",T,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	410 for(iFactor in 1:length(orderedFactors)){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	411 #if it is the last factor of the list or if all factor
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	412 if(iFactor==length(orderedFactors) \|\| allFactorsBigger){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	413 if(length(orderedFactors)==1 \|\| allFactorsBigger){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	414 dataToPlot=data.frame(PC1=PACres$x[,1],PC2=PACres$x[,2],PC3=PACres$x[,3],Experiments=rownames(PACres$x), Attribute1=factorInfoMatrix[rownames(PACres$x),orderedFactors[iFactor]], hoverLabel=unlist(lapply(rownames(PACres$x),function(x)paste(factorInfoMatrix[x,-1],collapse=","))))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	415 p <- plot_ly(dataToPlot,x = ~PC1, y = ~PC2, z = ~PC3, type = 'scatter3d', mode="markers", color=~Attribute1,colors=rainbow(length(levels(dataToPlot$Attribute1))+2),hoverinfo = 'text', text = ~paste(Experiments,"\n",hoverLabel),marker=list(size=5))%>%
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	416 layout(title = "Principal Component Analysis", scene = list(xaxis = list(title = "Component 1"),yaxis = list(title = "Component 2"),zaxis = list(title = "Component 3")),
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	417 legend=list(font = list(family = "sans-serif",size = 15,color = "#000")))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	418 fileIdent=correspondanceNameTable[orderedFactors[iFactor],1]
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	419 #add text label to plot
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	420 ##p <- add_text(p,x = dataToPlot$PC1, y = dataToPlot$PC2 + (max(PACres$x[,2])-min(PACres$x[,2]))*0.02, z = dataToPlot$PC3, mode = 'text', inherit = F, text=rownames(PACres$x), hoverinfo='skip', showlegend = FALSE, color=I('black'))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	421 #save the plotly plot
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	422 htmlwidgets::saveWidget(as_widget(p), paste(c(file.path(getwd(), "plotLyDir"),"/",opt$acp,"_",fileIdent,".html"),collapse=""),selfcontained = F)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	423 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	424 }else{
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	425 for(iFactorBis in (iFactor+1):length(orderedFactors)){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	426 if(length(table(factorInfoMatrix[,orderedFactors[iFactorBis]]))<=length(symbolset)){
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	427 dataToPlot=data.frame(PC1=PACres$x[,1],PC2=PACres$x[,2],PC3=PACres$x[,3],Experiments=rownames(PACres$x), Attribute1=factorInfoMatrix[rownames(PACres$x),orderedFactors[iFactor]], Attribute2=factorInfoMatrix[rownames(PACres$x),orderedFactors[iFactorBis]], hoverLabel=unlist(lapply(rownames(PACres$x),function(x)paste(factorInfoMatrix[x,-1],collapse=","))))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	428 p <- plot_ly(dataToPlot,x = ~PC1, y = ~PC2, z = ~PC3, type = 'scatter3d', mode="markers", color=~Attribute1,colors=rainbow(length(levels(dataToPlot$Attribute1))+2),symbol=~Attribute2,symbols = symbolset,hoverinfo = 'text', text = ~paste(Experiments,"\n",hoverLabel),marker=list(size=5))%>%
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	429 layout(title = "Principal Component Analysis", scene = list(xaxis = list(title = "Component 1"),yaxis = list(title = "Component 2"),zaxis = list(title = "Component 3")),
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	430 legend=list(font = list(family = "sans-serif",size = 15,color = "#000")))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	431 fileIdent=paste(correspondanceNameTable[orderedFactors[c(iFactor,iFactorBis)],1],collapse="_AND_")
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	432 #add text label to plot
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	433 ##p <- add_text(p,x = dataToPlot$PC1, y = dataToPlot$PC2 + (max(PACres$x[,2])-min(PACres$x[,2]))*0.02, z = dataToPlot$PC3, mode = 'text', inherit = F, text=rownames(PACres$x), hoverinfo='skip', showlegend = FALSE, color=I('black'))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	434 #save the plotly plot
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	435 htmlwidgets::saveWidget(as_widget(p), paste(c(file.path(getwd(), "plotLyDir"),"/",opt$acp,"_",fileIdent,".html"),collapse=""),selfcontained = F)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	436 }else{
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	437 addComment(c("[WARNING]PCA with",orderedFactors[iFactor],"and",orderedFactors[iFactorBis],"groups cannot be displayed, too many groups (max",length(symbolset),")"),T,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	438 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	439 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	440 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	441 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	442 }else{
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	443 dataToPlot=data.frame(PC1=PACres$x[,1],PC2=PACres$x[,2],PC3=PACres$x[,3],Experiments=rownames(PACres$x))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	444 p <- plot_ly(dataToPlot,x = ~PC1, y = ~PC2, z = ~PC3, type = 'scatter3d', mode="markers",marker=list(size=5,color="salmon"),hoverinfo = 'text',text = ~paste(Experiments))%>%
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	445 layout(title = "Principal Component Analysis", scene = list(xaxis = list(title = "Component 1"),yaxis = list(title = "Component 2"),zaxis = list(title = "Component 3")),
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	446 legend=list(font = list(family = "sans-serif",size = 15,color = "#000")))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	447 ##p <- add_text(p,x = dataToPlot$PC1, y = dataToPlot$PC2 + (max(PACres$x[,2])-min(PACres$x[,2]))*0.02, z = dataToPlot$PC3, mode = 'text', inherit = F, text=rownames(PACres$x), hoverinfo='skip', showlegend = FALSE, color=I('black'))
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	448
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	449 #save plotly files
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	450 htmlwidgets::saveWidget(as_widget(p), paste(c(file.path(getwd(), "plotLyDir"),"/",opt$acp,"_plot.html"),collapse=""),selfcontained = F)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	451 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	452 remove(p,dataToPlot,dataFiltered)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	453 addComment("[INFO]ACP plot drawn",T,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	454 }
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	455
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	456 #write correspondances between plot file names and displayed names in figure legends, usefull to define html items in xml file
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	457 write.table(correspondanceNameTable,file=file.path(getwd(), "correspondanceFileNames.csv"),quote=FALSE,sep="\t",col.names = F,row.names = F)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	458
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	459 end.time <- Sys.time()
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	460 addComment(c("[INFO]Total execution time for R script:",as.numeric(end.time - start.time,units="mins"),"mins"),T,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	461
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	462 addComment("[INFO]End of R script",T,opt$log,display=FALSE)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	463
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	464 printSessionInfo(opt$log)
c9a38c1eadf1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	465 #sessionInfo()

Mercurial > repos > vandelj > giant_volcano_plot

annotate src/ExprPlotsScript.R @ 0:c9a38c1eadf1 draft