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comparison ImportDataFromMatrix.R @ 0:1024245abc70 draft

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
author sblanck
date Thu, 22 Feb 2018 08:38:22 -0500
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children 3ce32282f6a4
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-1:000000000000 0:1024245abc70
1 #!/usr/bin/env Rscript
2 # setup R error handling to go to stderr
3 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
4
5 # we need that to not crash galaxy with an UTF8 error on German LC settings.
6 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
7
8 library("optparse")
9
10 ##### Read options
11 option_list=list(
12 make_option("--input",type="character",default="NULL",help="rdata object containing eset object"),
13 make_option("--conditions",type="character",default=NULL,help="Text file summarizing conditions of the experiment (required)"),
14 make_option("--normalization",type="character",default=NULL,help="log2 transformation"),
15 make_option("--annotations",type="character",default="NULL",help="rdata object containing eset object"),
16 make_option("--rdataoutput",type="character",default="NULL",help="output rdata object containing eset object"),
17 make_option("--htmloutput",type="character",default=NULL,help="Output html report"),
18 make_option("--htmloutputpath",type="character",default="NULL",help="Path of output html report"),
19 make_option("--htmltemplate",type="character",default="NULL",help="html template)")
20
21
22 );
23
24
25 opt_parser = OptionParser(option_list=option_list);
26 opt = parse_args(opt_parser);
27
28 if(is.null(opt$input)){
29 print_help(opt_parser)
30 stop("input required.", call.=FALSE)
31 }
32
33 if(is.null(opt$conditions)){
34 print_help(opt_parser)
35 stop("conditions input required.", call.=FALSE)
36 }
37
38
39 #loading libraries
40 suppressPackageStartupMessages(require(GEOquery))
41
42 suppressPackageStartupMessages(require(Biobase))
43 suppressPackageStartupMessages(require(GEOquery))
44 suppressPackageStartupMessages(require(GEOmetadb))
45 suppressPackageStartupMessages(require(limma))
46 suppressPackageStartupMessages(require(jsonlite))
47 suppressPackageStartupMessages(require(affy))
48 suppressPackageStartupMessages(require(dplyr))
49 suppressPackageStartupMessages(require(affyPLM))
50
51 dataFile=opt$input
52 normalization=opt$normalization
53 conditionsFile=opt$conditions
54 annotation=opt$annotations
55 result_export_eset=opt$rdataoutput
56 result=opt$htmloutput
57 result.path=opt$htmloutputpath
58 result.template=opt$htmltemplate
59
60 dir.create(result.path, showWarnings = TRUE, recursive = FALSE)
61
62 data=as.matrix(read.table(file = dataFile,row.names=1,header=TRUE))
63 conditions=read.table(file=conditionsFile,sep = "\t",row.names=1)
64 htmlfile=readChar(result.template, file.info(result.template)$size)
65
66 colnames(conditions)=c("source_name_ch1","description")
67 phenodata<-new("AnnotatedDataFrame",data=conditions)
68
69 head(data)
70 conditions
71
72 eset=ExpressionSet(assayData=data,phenoData=phenodata,annotation=annotation)
73
74 if (normalization == "quantile") {
75 eset <- normalize.ExpressionSet.quantiles(eset, transfn="log2")
76 } else if (normalization == "log2") {
77 exprs(eset) = log2(exprs(eset))
78 }
79
80 boxplotnorm="boxplotnorm.png"
81 png(boxplotnorm,width=800,height = 400)
82 par(mar=c(7,5,1,1))
83 boxplot(data.frame(exprs(eset)),las=2,outline=FALSE)
84 dev.off()
85 htmlfile=gsub(x=htmlfile,pattern = "###BOXPLOTNORM###",replacement = boxplotnorm, fixed = TRUE)
86 file.copy(boxplotnorm,result.path)
87
88 plotMAnorm="plotMAnorm.png"
89 nblines=length(colnames(data))%/%3 + as.numeric((length(colnames(data))%%3)!=0)
90 png(plotMAnorm,width=800,height =300*nblines )
91 par(mfrow=c(nblines,3))
92 ##for (i in 1:length(colnames(data))){
93 MAplot(eset)
94 #}
95
96 dev.off()
97 htmlfile=gsub(x=htmlfile,pattern = "###PLOTMANORM###",replacement = plotMAnorm, fixed = TRUE)
98 file.copy(plotMAnorm,result.path)
99 #write.table(tolower(c(condition1Name,condition2Name)),quote = FALSE,col.names = FALSE, row.names=FALSE,file=result_export_conditions)
100 #saveConditions=c(condition1Name,condition2Name)
101 save(eset,file=result_export_eset)
102 write(htmlfile,result)
103
104 #l=list()
105 #for(i in 1:length(esets))
106 #{
107 # l[[paste("study",i,sep="")]]<-res[[i]]
108 #}
109 #l[["Meta"]]=res[[length(res)-1]]
110 #showVenn(res,file.path(temp.files.path,"venn.png"))
111 #writeLines(c("<h2>Venn diagram</h2>"),file.conn)
112 #writeLines(c("<img src='venn.png'><br/><br/>"),file.conn)
113 #writeLines(c("</body></html>"),file.conn)
114 #close(file.conn)