proteore_topgo: enrichment

annotate enrichment_v3.R @ 5:829cbdb71efa draft

planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty

author	proteore
date	Thu, 01 Mar 2018 11:04:54 -0500
parents	472ad7da3d92
children	ddaa0c318d65

rev	line source
0 472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	1 # enrichment_v3.R
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	2 # Usage : Rscript --vanilla enrichment_v3.R --inputtype tabfile (or
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	3 # copypaste) --input file.txt --ontology "BP/CC/MF" --option option (e.g
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	4 # : classic/elim...) --threshold threshold --correction correction --textoutput
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	5 # text --barplotoutput barplot
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	6 # --dotplotoutput dotplot --column column --geneuniver human
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	7 # e.g : Rscript --vanilla enrichment_v3.R --inputtype tabfile --input file.txt
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	8 # --ontology BP --option classic --threshold 1e-15 --correction holm
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	9 # --textoutput TRUE
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	10 # --barplotoutput TRUE --dotplotoutput TRUE --column c1 --geneuniverse
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	11 # org.Hs.eg.db
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	12 # INPUT :
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	13 # - type of input. Can be ids separated by a blank space (copypast), or a text
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	14 # file (tabfile)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	15 # - file with at least one column of ensembl ids
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	16 # - gene ontology category : Biological Process (BP), Cellular Component (CC), Molecular Function (MF)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	17 # - test option (relative to topGO algorithms) : elim, weight01, parentchild, or no option (classic)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	18 # - threshold for enriched GO term pvalues (e.g : 1e-15)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	19 # - correction for multiple testing (see p.adjust options : holm, hochberg, hommel, bonferroni, BH, BY,fdr,none
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	20 # - outputs wanted in this order text, barplot, dotplot with boolean value (e.g
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	21 # : TRUE TRUE TRUE ).
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	22 # Declare the output not wanted as none
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	23 # - column containing the ensembl ids if the input file is a tabfile
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	24 # - gene universe reference for the user chosen specie
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	25 # - header : if the input is a text file, does this text file have a header
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	26 # (TRUE/FALSE)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	27 #
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	28 # OUTPUT :
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	29 # - outputs commanded by the user named respectively result.tsv for the text
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	30 # results file, barplot.png for the barplot image file and dotplot.png for the
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	31 # dotplot image file
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	32
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	33
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	34 # loading topGO library
5 829cbdb71efa planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: 0 diff changeset	35 library(topGO)
0 472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	36
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	37 '%!in%' <- function(x,y)!('%in%'(x,y))
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	38
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	39
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	40 # Parse command line arguments
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	41
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	42 args = commandArgs(trailingOnly = TRUE)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	43
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	44 # create a list of the arguments from the command line, separated by a blank space
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	45 hh <- paste(unlist(args),collapse=' ')
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	46
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	47 # delete the first element of the list which is always a blank space
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	48 listoptions <- unlist(strsplit(hh,'--'))[-1]
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	49
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	50 # for each input, split the arguments with blank space as separator, unlist,
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	51 # and delete the first element which is the input name (e.g --inputtype)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	52 options.args <- sapply(listoptions,function(x){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	53 unlist(strsplit(x, ' '))[-1]
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	54 })
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	55 # same as the step above, except that only the names are kept
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	56 options.names <- sapply(listoptions,function(x){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	57 option <- unlist(strsplit(x, ' '))[1]
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	58 })
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	59 names(options.args) <- unlist(options.names)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	60
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	61
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	62 if (length(options.args) != 12) {
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	63 stop("Not enough/Too many arguments", call. = FALSE)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	64 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	65
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	66 typeinput = options.args[1]
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	67 listfile = options.args[2]
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	68 onto = as.character(options.args[3])
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	69 option = as.character(options.args[4])
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	70 correction = as.character(options.args[6])
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	71 threshold = as.numeric(options.args[5])
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	72 text = as.character(options.args[7])
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	73 barplot = as.character(options.args[8])
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	74 dotplot = as.character(options.args[9])
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	75 column = as.numeric(gsub("c","",options.args[10]))
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	76 geneuniverse = as.character(options.args[11])
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	77 header = as.character(options.args[12])
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	78
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	79 if (typeinput=="copypaste"){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	80 sample = as.data.frame(unlist(listfile))
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	81 sample = sample[,column]
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	82 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	83 if (typeinput=="tabfile"){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	84
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	85 if (header=="TRUE"){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	86 sample = read.table(listfile,header=TRUE,sep="\t",na.strings="NA",fill=TRUE)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	87 }else{
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	88 sample = read.table(listfile,header=FALSE,sep="\t",na.strings="NA",fill=TRUE)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	89 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	90 sample = sample[,column]
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	91
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	92 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	93 # Launch enrichment analysis and return result data from the analysis or the null
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	94 # object if the enrichment could not be done.
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	95 goEnrichment = function(geneuniverse,sample,onto){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	96
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	97 # get all the GO terms of the corresponding ontology (BP/CC/MF) and all their
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	98 # associated ensembl ids according to the org package
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	99 xx = annFUN.org(onto,mapping=geneuniverse,ID="ensembl")
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	100 allGenes = unique(unlist(xx))
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	101 # check if the genes given by the user can be found in the org package (gene
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	102 # universe), that is in
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	103 # allGenes
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	104 if (length(intersect(sample,allGenes))==0){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	105
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	106 print("None of the input ids can be found in the org package data, enrichment analysis cannot be realized. \n The inputs ids probably have no associated GO terms.")
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	107 return(c(NULL,NULL))
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	108
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	109 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	110
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	111 geneList = factor(as.integer(allGenes %in% sample))
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	112 names(geneList) <- allGenes
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	113
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	114
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	115 #topGO enrichment
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	116
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	117
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	118 # Creation of a topGOdata object
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	119 # It will contain : the list of genes of interest, the GO annotations and the GO hierarchy
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	120 # Parameters :
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	121 # ontology : character string specifying the ontology of interest (BP, CC, MF)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	122 # allGenes : named vector of type numeric or factor
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	123 # annot : tells topGO how to map genes to GO annotations.
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	124 # argument not used here : nodeSize : at which minimal number of GO annotations
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	125 # do we consider a gene
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	126
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	127 myGOdata = new("topGOdata", description="SEA with TopGO", ontology=onto, allGenes=geneList, annot = annFUN.org, mapping=geneuniverse,ID="ensembl")
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	128
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	129
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	130 # Performing enrichment tests
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	131 result <- runTest(myGOdata, algorithm=option, statistic="fisher")
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	132 return(c(result,myGOdata))
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	133 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	134
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	135 # Some libraries such as GOsummaries won't be able to treat the values such as
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	136 # "< 1e-30" produced by topGO. As such it is important to delete the < char
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	137 # with the deleteInfChar function. Nevertheless the user will have access to the original results in the text output.
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	138 deleteInfChar = function(values){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	139
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	140 lines = grep("<",values)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	141 if (length(lines)!=0){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	142 for (line in lines){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	143 values[line]=gsub("<","",values[line])
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	144 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	145 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	146 return(values)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	147 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	148
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	149 corrMultipleTesting = function(result, myGOdata,correction,threshold){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	150
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	151 # adjust for multiple testing
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	152 if (correction!="none"){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	153 # GenTable : transforms the result object into a list. Filters can be applied
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	154 # (e.g : with the topNodes argument, to get for instance only the n first
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	155 # GO terms with the lowest pvalues), but as we want to apply a correction we
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	156 # take all the GO terms, no matter their pvalues
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	157 allRes <- GenTable(myGOdata, test = result, orderBy = "result", ranksOf = "result",topNodes=length(attributes(result)$score))
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	158 # Some pvalues given by topGO are not numeric (e.g : "<1e-30). As such, these
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	159 # values are converted to 1e-30 to be able to correct the pvalues
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	160 pvaluestmp = deleteInfChar(allRes$test)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	161
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	162 # the correction is done from the modified pvalues
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	163 allRes$qvalues = p.adjust(pvaluestmp, method = as.character(correction), n = length(pvaluestmp))
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	164 allRes = as.data.frame(allRes)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	165
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	166 # Rename the test column by pvalues, so that is more explicit
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	167 nb = which(names(allRes) %in% c("test"))
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	168
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	169 names(allRes)[nb] = "pvalues"
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	170
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	171 allRes = allRes[which(as.numeric(allRes$pvalues) <= threshold),]
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	172 if (length(allRes$pvalues)==0){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	173 print("Threshold was too stringent, no GO term found with pvalue equal or lesser than the threshold value")
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	174 return(NULL)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	175 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	176 allRes = allRes[order(allRes$qvalues),]
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	177 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	178
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	179 if (correction=="none"){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	180 # get all the go terms under user threshold
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	181 mysummary <- summary(attributes(result)$score <= threshold)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	182 numsignif <- as.integer(mysummary[[3]])
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	183 # get all significant nodes
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	184 allRes <- GenTable(myGOdata, test = result, orderBy = "result", ranksOf = "result",topNodes=numsignif)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	185
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	186
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	187 allRes = as.data.frame(allRes)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	188 # Rename the test column by pvalues, so that is more explicit
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	189 nb = which(names(allRes) %in% c("test"))
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	190 names(allRes)[nb] = "pvalues"
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	191 if (numsignif==0){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	192
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	193 print("Threshold was too stringent, no GO term found with pvalue equal or lesser than the threshold value")
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	194 return(NULL)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	195 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	196
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	197 allRes = allRes[order(allRes$pvalues),]
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	198 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	199
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	200 return(allRes)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	201 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	202
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	203 # roundValues will simplify the results by rounding down the values. For instance 1.1e-17 becomes 1e-17
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	204 roundValues = function(values){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	205 for (line in 1:length(values)){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	206 values[line]=as.numeric(gsub(".*e","1e",as.character(values[line])))
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	207 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	208 return(values)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	209 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	210
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	211 createDotPlot = function(data, onto){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	212
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	213 values = deleteInfChar(data$pvalues)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	214 values = roundValues(values)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	215 values = as.numeric(values)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	216
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	217 geneRatio = data$Significant/data$Annotated
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	218 goTerms = data$Term
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	219 count = data$Significant
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	220
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	221 labely = paste("GO terms",onto,sep=" ")
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	222 png(filename="dotplot.png",res=300, width = 3200, height = 3200, units = "px")
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	223 sp1 = ggplot(data,aes(x=geneRatio,y=goTerms, color=values,size=count)) +geom_point() + scale_colour_gradientn(colours=c("red","violet","blue")) + xlab("Gene Ratio") + ylab(labely) + labs(color="p-values\n")
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	224
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	225 plot(sp1)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	226 dev.off()
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	227 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	228
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	229 createBarPlot = function(data, onto){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	230
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	231
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	232 values = deleteInfChar(data$pvalues)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	233 values = roundValues(values)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	234
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	235 values = as.numeric(values)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	236 goTerms = data$Term
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	237 count = data$Significant
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	238 png(filename="barplot.png",res=300, width = 3200, height = 3200, units = "px")
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	239
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	240 labely = paste("GO terms",onto,sep=" ")
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	241 p<-ggplot(data, aes(x=goTerms, y=count,fill=values)) + ylab("Gene count") + xlab(labely) +geom_bar(stat="identity") + scale_fill_gradientn(colours=c("red","violet","blue")) + coord_flip() + labs(fill="p-values\n")
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	242 plot(p)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	243 dev.off()
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	244 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	245
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	246
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	247 # Produce the different outputs
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	248 createOutputs = function(result, cut_result,text, barplot, dotplot, onto){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	249
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	250
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	251 if (is.null(result)){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	252
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	253 if (text=="TRUE"){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	254
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	255 err_msg = "None of the input ids can be found in the org package data, enrichment analysis cannot be realized. \n The inputs ids probably either have no associated GO terms or are not ENSG identifiers (e.g : ENSG00000012048)."
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	256 write.table(err_msg, file='result.csv', quote=FALSE, sep='\t', col.names = T, row.names = F)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	257
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	258 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	259
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	260 if (barplot=="TRUE"){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	261
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	262 png(filename="barplot.png")
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	263 plot.new()
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	264 #text(0,0,err_msg)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	265 dev.off()
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	266 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	267
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	268 if (dotplot=="TRUE"){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	269
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	270 png(filename="dotplot.png")
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	271 plot.new()
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	272 #text(0,0,err_msg)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	273 dev.off()
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	274
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	275 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	276 return(TRUE)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	277 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	278
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	279
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	280 if (is.null(cut_result)){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	281
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	282
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	283 if (text=="TRUE"){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	284
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	285 err_msg = "Threshold was too stringent, no GO term found with pvalue equal or lesser than the threshold value."
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	286 write.table(err_msg, file='result.csv', quote=FALSE, sep='\t', col.names = T, row.names = F)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	287
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	288 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	289
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	290 if (barplot=="TRUE"){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	291
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	292 png(filename="barplot.png")
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	293 plot.new()
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	294 text(0,0,err_msg)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	295 dev.off()
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	296 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	297
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	298 if (dotplot=="TRUE"){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	299
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	300 png(filename="dotplot.png")
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	301 plot.new()
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	302 text(0,0,err_msg)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	303 dev.off()
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	304
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	305 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	306 return(TRUE)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	307
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	308
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	309
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	310 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	311
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	312 if (text=="TRUE"){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	313 write.table(cut_result, file='result.csv', quote=FALSE, sep='\t', col.names = T, row.names = F)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	314 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	315
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	316 if (barplot=="TRUE"){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	317
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	318 createBarPlot(cut_result, onto)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	319 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	320
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	321 if (dotplot=="TRUE"){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	322
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	323 createDotPlot(cut_result, onto)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	324 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	325 return(TRUE)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	326 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	327
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	328
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	329
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	330 # Load R library ggplot2 to plot graphs
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	331 library(ggplot2)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	332
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	333 # Launch enrichment analysis
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	334 allresult = goEnrichment(geneuniverse,sample,onto)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	335 result = allresult[1][[1]]
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	336 myGOdata = allresult[2][[1]]
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	337 if (!is.null(result)){
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	338
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	339 # Adjust the result with a multiple testing correction or not and with the user
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	340 # p-value cutoff
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	341 cut_result = corrMultipleTesting(result,myGOdata, correction,threshold)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	342 }else{
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	343
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	344 cut_result=NULL
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	345
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	346 }
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	347
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	348
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	349 createOutputs(result, cut_result,text, barplot, dotplot, onto)
472ad7da3d92 planemo upload commit 9f9e8b72a239e58b5087b2b3737262c25cc2671e-dirty proteore parents: diff changeset	350

Mercurial > repos > proteore > proteore_topgo

annotate enrichment_v3.R @ 5:829cbdb71efa draft