giant_limma_analysis: src/VolcanoPlotsScript.R annotate

annotate src/VolcanoPlotsScript.R @ 0:f274c8d45613 draft

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

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

rev	line source
0 f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	1 # R script to plot volcanos through Galaxy based GIANT tool
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	2 # written by Jimmy Vandel
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	3 #
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	4 #
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	5 initial.options <- commandArgs(trailingOnly = FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	6 file.arg.name <- "--file="
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	7 script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)])
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	8 script.basename <- dirname(script.name)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	9 source(file.path(script.basename, "utils.R"))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	10 source(file.path(script.basename, "getopt.R"))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	11
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	12 #addComment("Welcome R!")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	13
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	14 # setup R error handling to go to stderr
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	15 options( show.error.messages=F, error = function () { cat(geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	16
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	17 # we need that to not crash galaxy with an UTF8 error on German LC settings.
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	18 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	19 loc <- Sys.setlocale("LC_NUMERIC", "C")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	20
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	21 #get starting time
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	22 start.time <- Sys.time()
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	23
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	24 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	25 args <- commandArgs()
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	26
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	27 # get options, using the spec as defined by the enclosed list.
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	28 # we read the options from the default: commandArgs(TRUE).
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	29 spec <- matrix(c(
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	30 "statisticsFile", "i", 1, "character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	31 "volcanoName" , "n", 1, "character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	32 "pvalColumnName" , "p", 1, "character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	33 "fdrColumnName" , "m", 1, "character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	34 "fcColumnName" , "c", 1, "character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	35 "fcKind","d", 1, "character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	36 "fdrThreshold","s", 1, "double",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	37 "fcThreshold","e", 1, "double",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	38 "organismID","x",1,"character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	39 "rowNameType","y",1,"character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	40 "log", "l", 1, "character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	41 "outputFile" , "o", 1, "character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	42 "format", "f", 1, "character",
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	43 "quiet", "q", 0, "logical"),
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	44 byrow=TRUE, ncol=4)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	45 opt <- getopt(spec)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	46
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	47 # enforce the following required arguments
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	48 if (is.null(opt$log)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	49 addComment("[ERROR]'log file' is required\n")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	50 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	51 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	52 addComment("[INFO]Start of R script",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	53 if (is.null(opt$statisticsFile)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	54 addComment("[ERROR]'statisticsFile' is required",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	55 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	56 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	57 if (length(opt$pvalColumnName)==0 \|\| length(opt$fdrColumnName)==0 \|\| length(opt$fcColumnName)==0) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	58 addComment("[ERROR]no selected columns",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	59 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	60 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	61 if (length(opt$pvalColumnName)!=length(opt$fcColumnName) \|\| length(opt$pvalColumnName)!=length(opt$fdrColumnName)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	62 addComment("[ERROR]different number of selected columns between p.val, adj-p.val and FC ",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	63 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	64 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	65 if (is.null(opt$fcKind)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	66 addComment("[ERROR]'fcKind' is required",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	67 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	68 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	69 if (is.null(opt$fdrThreshold)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	70 addComment("[ERROR]'FDR threshold' is required",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	71 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	72 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	73 if (is.null(opt$fcThreshold)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	74 addComment("[ERROR]'FC threshold' is required",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	75 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	76 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	77 if (is.null(opt$outputFile)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	78 addComment("[ERROR]'output file' is required",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	79 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	80 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	81 if (is.null(opt$format)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	82 addComment("[ERROR]'output format' is required",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	83 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	84 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	85
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	86 #demande si le script sera bavard
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	87 verbose <- if (is.null(opt$quiet)) {
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	88 TRUE
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	89 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	90 FALSE
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	91 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	92
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	93 #paramètres internes
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	94 addComment("[INFO]Parameters checked test mode !",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	95
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	96 addComment(c("[INFO]Working directory: ",getwd()),TRUE,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	97 addComment(c("[INFO]Command line: ",args),TRUE,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	98
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	99 #directory for plots
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	100 dir.create(file.path(getwd(), "plotDir"))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	101 dir.create(file.path(getwd(), "plotLyDir"))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	102
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	103 #charge des packages silencieusement
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	104 suppressPackageStartupMessages({
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	105 library("methods")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	106 library("biomaRt")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	107 library("ggplot2")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	108 library("plotly")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	109 library("stringr")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	110 })
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	111
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	112 #define some usefull variable
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	113 nbVolcanosToPlot=length(opt$pvalColumnName)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	114
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	115 #load input file
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	116 statDataMatrix=read.csv(file=file.path(getwd(), opt$statisticsFile),header=F,sep="\t",colClasses="character")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	117 #remove first colum to convert it as rownames
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	118 rownames(statDataMatrix)=statDataMatrix[,1]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	119 statDataMatrix=statDataMatrix[,-1]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	120
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	121 #identify lines without adjusted p-value info (should contain the same content as rownames) and replace them with NA values
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	122 FDRinfo=rep(TRUE,nbVolcanosToPlot)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	123 for(iVolcano in 1:nbVolcanosToPlot){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	124 #input parameter should be None when adjusted p-val are not available
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	125 if(opt$fdrColumnName[iVolcano]=="None"){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	126 #content of the corresponding column should also be the same as rownames
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	127 if(!all(statDataMatrix[,(iVolcano-1)*3+2]==rownames(statDataMatrix))){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	128 addComment(c("[ERROR]It seems that input stat matrix contains adjusted p-values for volcano",iVolcano,"whereas input parameter indicates that not."),T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	129 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	130 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	131 FDRinfo[iVolcano]=FALSE
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	132 statDataMatrix[,(iVolcano-1)*3+2]=NA
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	133 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	134 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	135
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	136 if(is.data.frame(statDataMatrix)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	137 statDataMatrix=data.matrix(statDataMatrix)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	138 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	139 statDataMatrix=data.matrix(as.numeric(statDataMatrix))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	140 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	141
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	142 #check if available column number match with volcano requested number
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	143 if(ncol(statDataMatrix)!=3*nbVolcanosToPlot){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	144 addComment("[ERROR]Input file column number is different from requested volcano number",T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	145 q( "no", 1, F )
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	146 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	147
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	148 #build global dataFrame with data and fill with p.val and log2(FC) and FDR
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	149 dataFrame=data.frame(row.names = rownames(statDataMatrix))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	150 #start with p-value
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	151 dataFrame$p.value=statDataMatrix[,seq(1,nbVolcanosToPlot*3,3),drop=FALSE]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	152 #compute FDR if needed or just get available info
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	153 dataFrame$adj_p.value=dataFrame$p.value
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	154 for(iVolcano in 1:nbVolcanosToPlot){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	155 #adjusted p-value are already computed
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	156 if(FDRinfo[iVolcano]){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	157 dataFrame$adj_p.value[,iVolcano]=statDataMatrix[,(iVolcano-1)*3+2,drop=FALSE]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	158 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	159 #adjusted p-value should be computed based on p-val using FDR
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	160 dataFrame$adj_p.value[,iVolcano]=p.adjust(dataFrame$p.value[,iVolcano,drop=FALSE],"fdr")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	161 addComment(c("[INFO]Adjusted p-values are not available in input for volcano",iVolcano,", FDR approach will be used on available raw p-values"),T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	162 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	163 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	164 if(opt$fcKind=="FC"){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	165 #we should transform as Log2FC
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	166 dataFrame$coefficients=log2(statDataMatrix[,seq(3,nbVolcanosToPlot*3,3),drop=FALSE])
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	167 addComment(c("[INFO]FC are converted in log2(FC) for plotting"),T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	168 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	169 dataFrame$coefficients=statDataMatrix[,seq(3,nbVolcanosToPlot*3,3),drop=FALSE]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	170 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	171
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	172 addComment(c("[INFO]Input data available for",nbVolcanosToPlot,"volcano(s) with",nrow(statDataMatrix),"rows"),T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	173
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	174
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	175 #plot VOLCANOs
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	176 volcanoPerPage=1
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	177 logFCthreshold=log2(opt$fcThreshold)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	178 iToPlot=1
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	179 plotVector=list()
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	180 volcanoNameList=c()
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	181 for (iVolcano in 1:nbVolcanosToPlot){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	182
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	183 if(nchar(opt$volcanoName[iVolcano])>0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	184 curentVolcanoName=opt$volcanoName[iVolcano]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	185 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	186 curentVolcanoName=paste(iVolcano,opt$pvalColumnName[iVolcano],sep="_")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	187 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	188
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	189 #keep only rows without NA for p-val, adjusted p-val and coeff
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	190 pValToPlot=dataFrame$p.value[,iVolcano]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	191 fdrToPlot=dataFrame$adj_p.value[,iVolcano]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	192 coeffToPlot=dataFrame$coefficients[,iVolcano]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	193
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	194 rowToRemove=unique(c(which(is.na(pValToPlot)),which(is.na(fdrToPlot)),which(is.na(coeffToPlot))))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	195 if(length(rowToRemove)>0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	196 pValToPlot=pValToPlot[-rowToRemove]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	197 fdrToPlot=fdrToPlot[-rowToRemove]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	198 coeffToPlot=coeffToPlot[-rowToRemove]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	199 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	200 addComment(c("[INFO]For",curentVolcanoName,"volcano,",length(rowToRemove),"rows are discarded due to NA values,",length(pValToPlot),"remaining rows."),T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	201
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	202 #save volcano name
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	203 volcanoNameList=c(volcanoNameList,curentVolcanoName)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	204
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	205 #remove characters possibly troubling
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	206 volcanoFileName=iVolcano
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	207
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	208 #define the log10(p-val) threshold corresponding to FDR threshold fixed by user
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	209 probeWithLowFDR=-log10(pValToPlot[which(fdrToPlot<=opt$fdrThreshold)])
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	210 pvalThresholdFDR=NULL
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	211 if(length(probeWithLowFDR)>0)pvalThresholdFDR=min(probeWithLowFDR)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	212
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	213 #get significant points over FC and FDR thresholds
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	214 significativePoints=intersect(which(abs(coeffToPlot)>=logFCthreshold),which(fdrToPlot<=opt$fdrThreshold))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	215
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	216 #to reduce size of html plot, we keep 20000 points maximum sampled amongst genes with pval>=33%(pval) and abs(log2(FC))<=66%(abs(log2(FC)))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	217 htmlPointsToRemove=intersect(which(abs(coeffToPlot)<=quantile(abs(coeffToPlot),c(0.66))),which(pValToPlot>=quantile(abs(pValToPlot),c(0.33))))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	218 if(length(htmlPointsToRemove)>20000){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	219 htmlPointsToRemove=setdiff(htmlPointsToRemove,sample(htmlPointsToRemove,20000))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	220 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	221 htmlPointsToRemove=c()
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	222 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	223
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	224 xMinLimPlot=min(coeffToPlot)-0.2
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	225 xMaxLimPlot=max(coeffToPlot)+0.2
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	226 yMaxLimPlot= max(-log10(pValToPlot))+0.2
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	227
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	228 if(length(significativePoints)>0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	229 dataSignifToPlot=data.frame(pval=-log10(pValToPlot[significativePoints]),FC=coeffToPlot[significativePoints],description=paste(names(coeffToPlot[significativePoints]),"\n","FC: " , round(2^coeffToPlot[significativePoints],2) , " \| Adjusted p-val: ",prettyNum(fdrToPlot[significativePoints],digits=4), sep=""))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	230 #to test if remains any normal points to draw
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	231 if(length(significativePoints)<length(pValToPlot)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	232 dataToPlot=data.frame(pval=-log10(pValToPlot[-significativePoints]),FC=coeffToPlot[-significativePoints],description=paste("FC: " , round(2^coeffToPlot[-significativePoints],2) , " \| Adjusted p-val: ",prettyNum(fdrToPlot[-significativePoints],digits=4), sep=""))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	233 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	234 dataToPlot=data.frame(pval=0,FC=0,description="null")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	235 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	236 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	237 dataToPlot=data.frame(pval=-log10(pValToPlot),FC=coeffToPlot,description=paste("FC: " , round(2^coeffToPlot,2) , " \| Adjusted p-val: ",prettyNum(fdrToPlot,digits=4), sep=""))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	238 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	239
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	240 ##traditional plot
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	241
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	242 p <- ggplot(data=dataToPlot, aes(x=FC, y=pval)) + geom_point() +
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	243 theme_bw() + ggtitle(curentVolcanoName) + ylab(label="-Log10(p-val)") + xlab(label="Log2 Fold Change") +
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	244 theme(panel.border=element_blank(),plot.title = element_text(hjust = 0.5),legend.position="none")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	245 if(logFCthreshold!=0) p <- p + geom_vline(xintercept=-logFCthreshold, color="salmon",linetype="dotted", size=1) + geom_vline(xintercept=logFCthreshold, color="salmon",linetype="dotted", size=1) + geom_text(data.frame(text=c(paste(c("log2(1/FC=",opt$fcThreshold,")"),collapse=""),paste(c("log2(FC=",opt$fcThreshold,")"),collapse="")),x=c(-logFCthreshold,logFCthreshold),y=c(0,0)),mapping=aes(x=x, y=y, label=text), size=4, angle=90, vjust=-0.4, hjust=0, color="salmon")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	246 if(!is.null(pvalThresholdFDR)) p <- p + geom_hline(yintercept=pvalThresholdFDR, color="skyblue1",linetype="dotted", size=0.5) + geom_text(data.frame(text=c(paste(c("Adjusted pval limit(",opt$fdrThreshold,")"),collapse="")),x=c(xMinLimPlot),y=c(pvalThresholdFDR)),mapping=aes(x=x, y=y, label=text), size=4, vjust=0, hjust=0, color="skyblue3")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	247 if(length(significativePoints)>0)p <- p + geom_point(data=dataSignifToPlot,aes(colour=description))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	248
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	249 ##interactive plot
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	250
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	251 if(length(htmlPointsToRemove)>0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	252 pointToRemove=union(htmlPointsToRemove,significativePoints)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	253 #to test if it remains any normal points to draw
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	254 if(length(pointToRemove)<length(pValToPlot)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	255 dataToPlot=data.frame(pval=-log10(pValToPlot[-pointToRemove]),FC=coeffToPlot[-pointToRemove],description=paste("FC: " , round(2^coeffToPlot[-pointToRemove],2) , " \| Adjusted p-val: ", prettyNum(fdrToPlot[-pointToRemove],digits=4), sep=""))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	256 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	257 dataToPlot=data.frame(pval=0,FC=0,description="null")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	258 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	259 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	260
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	261 if((nrow(dataToPlot)+length(significativePoints))>40000)addComment(c("[WARNING]For",curentVolcanoName,"volcano, numerous points to plot(",nrow(dataToPlot)+nrow(dataSignifToPlot),"), resulting volcano could be heavy, using more stringent thresholds could be helpful."),T,opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	262
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	263 phtml <- plot_ly(data=dataToPlot, x=~FC, y=~pval,type="scatter", mode="markers",showlegend = FALSE, marker = list(color="gray",opacity=0.5), text=~description, hoverinfo="text") %>%
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	264 layout(title = curentVolcanoName[iVolcano],xaxis=list(title="Log2 Fold Change",showgrid=TRUE, zeroline=FALSE),yaxis=list(title="-Log10(p-val)", showgrid=TRUE, zeroline=FALSE))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	265 if(length(significativePoints)>0) phtml=add_markers(phtml,data=dataSignifToPlot, x=~FC, y=~pval, mode="markers" , marker=list( color=log10(abs(dataSignifToPlot$FC)*dataSignifToPlot$pval),colorscale='Rainbow'), text=~description, hoverinfo="text", inherit = FALSE) %>% hide_colorbar()
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	266 if(logFCthreshold!=0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	267 phtml=add_trace(phtml,x=c(-logFCthreshold,-logFCthreshold), y=c(0,yMaxLimPlot), type="scatter", mode = "lines", line=list(color="coral",dash="dash"), hoverinfo='none', showlegend = FALSE,inherit = FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	268 phtml=add_annotations(phtml,x=-logFCthreshold,y=0,xref = "x",yref = "y",text = paste(c("log2(1/FC=",opt$fcThreshold,")"),collapse=""),xanchor = 'right',showarrow = F,textangle=270,font=list(color="coral"))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	269 phtml=add_trace(phtml,x=c(logFCthreshold,logFCthreshold), y=c(0, yMaxLimPlot), type="scatter", mode = "lines", line=list(color="coral",dash="dash"), hoverinfo='none', showlegend = FALSE,inherit = FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	270 phtml=add_annotations(phtml,x=logFCthreshold,y=0,xref = "x",yref = "y",text = paste(c("log2(FC=",opt$fcThreshold,")"),collapse=""),xanchor = 'right',showarrow = F,textangle=270,font=list(color="coral"))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	271 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	272 if(!is.null(pvalThresholdFDR)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	273 phtml=add_trace(phtml,x=c(xMinLimPlot,xMaxLimPlot), y=c(pvalThresholdFDR,pvalThresholdFDR), type="scatter", mode = "lines", line=list(color="cornflowerblue",dash="dash"), hoverinfo='none', showlegend = FALSE,inherit = FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	274 phtml=add_annotations(phtml,x=xMinLimPlot,y=pvalThresholdFDR+0.1,xref = "x",yref = "y",text = paste(c("Adjusted pval limit(",opt$fdrThreshold,")"),collapse=""),xanchor = 'left',showarrow = F,font=list(color="cornflowerblue"))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	275 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	276 plotVector[[length(plotVector)+1]]=p
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	277
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	278 #save plotly files
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	279 pp <- ggplotly(phtml)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	280 htmlwidgets::saveWidget(as_widget(pp), paste(c(file.path(getwd(), "plotLyDir"),"/Volcanos_",volcanoFileName,".html"),collapse=""),selfcontained = F)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	281
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	282
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	283 if(iVolcano==nbVolcanosToPlot \|\| length(plotVector)==volcanoPerPage){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	284 #plot and close the actual plot
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	285 if(opt$format=="pdf"){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	286 pdf(paste(c("./plotDir/Volcanos_",volcanoFileName,".pdf"),collapse=""))}else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	287 png(paste(c("./plotDir/Volcanos_",volcanoFileName,".png"),collapse=""))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	288 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	289 multiplot(plotlist=plotVector,cols=1)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	290 dev.off()
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	291 if(iVolcano<nbVolcanosToPlot){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	292 #prepare for a new ploting file if necessary
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	293 plotVector=list()
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	294 iToPlot=iToPlot+1
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	295 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	296 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	297 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	298 remove(dataToPlot,dataSignifToPlot)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	299 addComment("[INFO]Volcanos drawn",T,opt$log,T,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	300
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	301
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	302 #now add anotation infos about genes
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	303
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	304 rowItemInfo=NULL
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	305 if(!is.null(opt$rowNameType) && !is.null(opt$organismID)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	306 ##get gene information from BioMart
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	307 #if(!require("biomaRt")){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	308 # source("https://bioconductor.org/biocLite.R")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	309 # biocLite("biomaRt")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	310 #}
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	311
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	312 ensembl_hs_mart <- useMart(biomart="ensembl", dataset=opt$organismID)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	313 ensembl_df <- getBM(attributes=c(opt$rowNameType,"description"),mart=ensembl_hs_mart)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	314 rowItemInfo=ensembl_df[which(ensembl_df[,1]!=""),2]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	315 rowItemInfo=unlist(lapply(rowItemInfo,function(x)substr(unlist(strsplit(x," \\[Source"))[1],1,30)))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	316 names(rowItemInfo)=ensembl_df[which(ensembl_df[,1]!=""),1]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	317 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	318
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	319 #filter out genes with higher p-values for all comparisons
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	320 genesToKeep=names(which(apply(dataFrame$adj_p.value,1,function(x)length(which(x<=opt$fdrThreshold))>0)))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	321 #filter out genes with lower FC for all comparisons
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	322 genesToKeep=intersect(genesToKeep,names(which(apply(dataFrame$coefficients,1,function(x)length(which(abs(x)>=logFCthreshold))>0))))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	323
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	324 if(length(genesToKeep)>0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	325 dataFrameNew=data.frame(row.names=genesToKeep)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	326
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	327 dataFrameNew$adj_p.value=matrix(dataFrame$adj_p.value[genesToKeep,,drop=FALSE],ncol=ncol(dataFrame$adj_p.value))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	328 rownames(dataFrameNew$adj_p.value)=genesToKeep
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	329 colnames(dataFrameNew$adj_p.value)=colnames(dataFrame$p.value)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	330
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	331 dataFrameNew$p.value=matrix(dataFrame$p.value[genesToKeep,,drop=FALSE],ncol=ncol(dataFrame$p.value))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	332 rownames(dataFrameNew$p.value)=genesToKeep
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	333 colnames(dataFrameNew$p.value)=colnames(dataFrame$adj_p.value)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	334
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	335 dataFrameNew$coefficients=matrix(dataFrame$coefficients[genesToKeep,,drop=FALSE],ncol=ncol(dataFrame$coefficients))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	336 rownames(dataFrameNew$coefficients)=genesToKeep
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	337 colnames(dataFrameNew$coefficients)=colnames(dataFrame$adj_p.value)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	338
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	339 dataFrame=dataFrameNew
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	340 rm(dataFrameNew)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	341 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	342 addComment("[WARNING]No significative genes",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	343 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	344
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	345 addComment("[INFO]Significant genes filtering done",T,opt$log,T,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	346
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	347
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	348 #plot VennDiagramm for genes below threshold between comparisons
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	349 #t=apply(dataFrame$adj_p.value[,1:4],2,function(x)names(which(x<=opt$threshold)))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	350 #get.venn.partitions(t)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	351 #vennCounts(dataFrame$adj_p.value[,1:4]<=opt$threshold)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	352
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	353 #make a simple sort genes based only on the first comparison
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	354 #newOrder=order(dataFrame$adj_p.value[,1])
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	355 #dataFrame$adj_p.value=dataFrame$adj_p.value[newOrder,]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	356
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	357 #alternative sorting strategy based on the mean gene rank over all comparisons
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	358 if(length(genesToKeep)>1){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	359 currentRank=rep(0,nrow(dataFrame$adj_p.value))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	360 for(iVolcano in 1:ncol(dataFrame$adj_p.value)){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	361 currentRank=currentRank+rank(dataFrame$adj_p.value[,iVolcano])
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	362 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	363 currentRank=currentRank/ncol(dataFrame$adj_p.value)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	364 newOrder=order(currentRank)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	365 rownames(dataFrame)=rownames(dataFrame)[newOrder]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	366
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	367 dataFrame$adj_p.value=matrix(dataFrame$adj_p.value[newOrder,],ncol=ncol(dataFrame$adj_p.value))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	368 rownames(dataFrame$adj_p.value)=rownames(dataFrame$p.value)[newOrder]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	369 colnames(dataFrame$adj_p.value)=colnames(dataFrame$p.value)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	370
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	371 dataFrame$p.value=matrix(dataFrame$p.value[newOrder,],ncol=ncol(dataFrame$p.value))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	372 rownames(dataFrame$p.value)=rownames(dataFrame$adj_p.value)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	373 colnames(dataFrame$p.value)=colnames(dataFrame$adj_p.value)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	374
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	375 dataFrame$coefficients=matrix(dataFrame$coefficients[newOrder,],ncol=ncol(dataFrame$coefficients))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	376 rownames(dataFrame$coefficients)=rownames(dataFrame$adj_p.value)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	377 colnames(dataFrame$coefficients)=colnames(dataFrame$adj_p.value)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	378 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	379
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	380 #formating output matrix depending on genes to keep
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	381 if(length(genesToKeep)==0){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	382 outputData=matrix(0,ncol=ncol(dataFrame$adj_p.value)*4+2,nrow=3)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	383 outputData[1,]=c("X","X",rep(volcanoNameList,each=4))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	384 outputData[2,]=c("X","X",rep(c("p-val","Adjusted.p-val","FC","log2(FC)"),ncol(dataFrame$adj_p.value)))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	385 outputData[,1]=c("Volcano","Gene","noGene")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	386 outputData[,2]=c("Comparison","Info","noInfo")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	387 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	388 if(length(genesToKeep)==1){
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	389 outputData=matrix(0,ncol=ncol(dataFrame$adj_p.value)*4+2,nrow=3)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	390 outputData[1,]=c("X","X",rep(volcanoNameList,each=4))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	391 outputData[2,]=c("X","X",rep(c("p-val","Adjusted.p-val","FC","log2(FC)"),ncol(dataFrame$adj_p.value)))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	392 outputData[,1]=c("Volcano","Gene",genesToKeep)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	393 outputData[,2]=c("Comparison","Info","na")
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	394 if(!is.null(rowItemInfo))outputData[3,2]=rowItemInfo[genesToKeep]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	395 outputData[3,seq(3,ncol(outputData),4)]=prettyNum(dataFrame$p.value,digits=4)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	396 outputData[3,seq(4,ncol(outputData),4)]=prettyNum(dataFrame$adj_p.value,digits=4)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	397 outputData[3,seq(5,ncol(outputData),4)]=prettyNum(2^dataFrame$coefficients,digits=4)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	398 outputData[3,seq(6,ncol(outputData),4)]=prettyNum(dataFrame$coefficients,digits=4)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	399 }else{
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	400 #format matrix to be correctly read by galaxy (move headers in first column and row)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	401 outputData=matrix(0,ncol=ncol(dataFrame$adj_p.value)*4+2,nrow=nrow(dataFrame$adj_p.value)+2)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	402 outputData[1,]=c("X","X",rep(volcanoNameList,each=4))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	403 outputData[2,]=c("X","X",rep(c("p-val","Adjusted.p-val","FC","log2(FC)"),ncol(dataFrame$adj_p.value)))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	404 outputData[,1]=c("Volcano","Gene",rownames(dataFrame$adj_p.value))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	405 outputData[,2]=c("Comparison","Info",rep("na",nrow(dataFrame$adj_p.value)))
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	406 if(!is.null(rowItemInfo))outputData[3:nrow(outputData),2]=rowItemInfo[rownames(dataFrame$adj_p.value)]
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	407 outputData[3:nrow(outputData),seq(3,ncol(outputData),4)]=prettyNum(dataFrame$p.value,digits=4)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	408 outputData[3:nrow(outputData),seq(4,ncol(outputData),4)]=prettyNum(dataFrame$adj_p.value,digits=4)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	409 outputData[3:nrow(outputData),seq(5,ncol(outputData),4)]=prettyNum(2^dataFrame$coefficients,digits=4)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	410 outputData[3:nrow(outputData),seq(6,ncol(outputData),4)]=prettyNum(dataFrame$coefficients,digits=4)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	411 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	412 }
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	413 addComment("[INFO]Formated output",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	414
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	415 #write output results
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	416 write.table(outputData,file=opt$outputFile,quote=FALSE,sep="\t",col.names = F,row.names = F)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	417
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	418
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	419 end.time <- Sys.time()
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	420 addComment(c("[INFO]Total execution time for R script:",as.numeric(end.time - start.time,units="mins"),"mins"),T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	421
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	422 addComment("[INFO]End of R script",T,opt$log,display=FALSE)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	423
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	424 printSessionInfo(opt$log)
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	425
f274c8d45613 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df" vandelj parents: diff changeset	426 #sessionInfo()

Mercurial > repos > vandelj > giant_limma_analysis

annotate src/VolcanoPlotsScript.R @ 0:f274c8d45613 draft