Mercurial > repos > proteore > proteore_topgo

comparison enrichment_v3.R @ 8:ddaa0c318d65 draft

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planemo upload commit d23909db127a655212b79d6826033889812f59b5-dirty
author proteore
date Fri, 23 Mar 2018 10:43:32 -0400
parents 829cbdb71efa
children 70c0c8757f5f
comparison
equal deleted inserted replaced
7:1b2b81169c66 8:ddaa0c318d65
30 # results file, barplot.png for the barplot image file and dotplot.png for the 30 # results file, barplot.png for the barplot image file and dotplot.png for the
31 # dotplot image file 31 # dotplot image file
32 32
33 33
34 # loading topGO library 34 # loading topGO library
35 library(topGO) 35 library(topGO)
36
37 # Read file and return file content as data.frame
38 readfile = function(filename, header) {
39 if (header == "true") {
40 # Read only first line of the file as header:
41 headers <- read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
42 #Read the data of the files (skipping the first row)
43 file <- read.table(filename, skip = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
44 # Remove empty rows
45 file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
46 #And assign the header to the data
47 names(file) <- headers
48 }
49 else {
50 file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
51 # Remove empty rows
52 file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
53 }
54 return(file)
55 }
36 56
37 '%!in%' <- function(x,y)!('%in%'(x,y)) 57 '%!in%' <- function(x,y)!('%in%'(x,y))
38 58
39 59
40 # Parse command line arguments 60 # Parse command line arguments
48 listoptions <- unlist(strsplit(hh,'--'))[-1] 68 listoptions <- unlist(strsplit(hh,'--'))[-1]
49 69
50 # for each input, split the arguments with blank space as separator, unlist, 70 # for each input, split the arguments with blank space as separator, unlist,
51 # and delete the first element which is the input name (e.g --inputtype) 71 # and delete the first element which is the input name (e.g --inputtype)
52 options.args <- sapply(listoptions,function(x){ 72 options.args <- sapply(listoptions,function(x){
53 unlist(strsplit(x, ' '))[-1] 73 unlist(strsplit(x, '[ \t\n]+'))[-1]
54 }) 74 })
55 # same as the step above, except that only the names are kept 75 # same as the step above, except that only the names are kept
56 options.names <- sapply(listoptions,function(x){ 76 options.names <- sapply(listoptions,function(x){
57 option <- unlist(strsplit(x, ' '))[1] 77 option <- unlist(strsplit(x, '[ \t\n]+'))[1]
58 }) 78 })
59 names(options.args) <- unlist(options.names) 79 names(options.args) <- unlist(options.names)
60 80
61 81
62 if (length(options.args) != 12) { 82 if (length(options.args) != 12) {
81 sample = sample[,column] 101 sample = sample[,column]
82 } 102 }
83 if (typeinput=="tabfile"){ 103 if (typeinput=="tabfile"){
84 104
85 if (header=="TRUE"){ 105 if (header=="TRUE"){
86 sample = read.table(listfile,header=TRUE,sep="\t",na.strings="NA",fill=TRUE) 106 sample = readfile(listfile, "true")
87 }else{ 107 }else{
88 sample = read.table(listfile,header=FALSE,sep="\t",na.strings="NA",fill=TRUE) 108 sample = readfile(listfile, "false")
89 } 109 }
90 sample = sample[,column] 110 sample = sample[,column]
91 111
92 } 112 }
93 # Launch enrichment analysis and return result data from the analysis or the null 113 # Launch enrichment analysis and return result data from the analysis or the null