Mercurial > repos > qfabrepo > metadegalaxy_phyloseq_deseq2

comparison phyloseq_2_deseq2.r @ 0:1f0569e94be4 draft

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"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
author qfabrepo
date Mon, 14 Sep 2020 08:20:41 +0000
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-1:000000000000 0:1f0569e94be4
1 library('getopt')
2 suppressPackageStartupMessages(library('phyloseq'))
3 suppressPackageStartupMessages(library('DESeq2'))
4
5 options(warn= -1)
6
7 option_specification = matrix(c(
8 'biomfile','b',2,'character',
9 'metafile','m',2,'character',
10 'factor','f',2,'numeric',
11 'test','t',2,'character',
12 'fitType','T',2,'character',
13 'cutoff','c','2','double',
14 'outdir','o',2,'character',
15 'result','r',2,'character',
16 'normalisedResult','n','2','character'
17 ),byrow=TRUE,ncol=4);
18
19
20 options <- getopt(option_specification);
21 options(bitmapType="cairo")
22
23
24 if (!is.null(options$outdir)) {
25 # Create the directory
26 dir.create(options$outdir,FALSE)
27 }
28
29
30 galaxy_biom <- import_biom(options$biomfile)
31 galaxy_map <- import_qiime_sample_data(options$metafile)
32 tax_col_norm <- c("Kingdom","Phylum","Class","Order","Family","Genus","Species")
33 tax_col_extra <- c("None","Kingdom","Phylum","Class","Order","Family","Genus","Species")
34
35 number.of.tax.rank<-length(colnames(tax_table(galaxy_biom)))
36
37 if( number.of.tax.rank == 7){
38 colnames(tax_table(galaxy_biom)) <- tax_col_norm
39 }else{
40 colnames(tax_table(galaxy_biom)) <- tax_col_extra
41 }
42
43
44 AIP_galaxy <- merge_phyloseq(galaxy_biom,galaxy_map)
45
46
47 Infactor<-colnames(galaxy_map)[options$factor]
48 method<-options$test
49 Type<-options$fitType
50 cutoff<-options$cutoff
51
52
53
54 suppressMessages(deseq2_obj<-phyloseq_to_deseq2(AIP_galaxy,as.formula(paste('~',Infactor,sep=""))))
55 gm_mean = function(x, na.rm=TRUE){
56 exp(sum(log(x[x > 0]), na.rm=na.rm) / length(x))
57 }
58 geoMeans = apply(counts(deseq2_obj), 1, gm_mean)
59 deseq2_obj = estimateSizeFactors(deseq2_obj, geoMeans = geoMeans)
60
61
62
63 ### Normalisation
64 deseq2_obj_norm<-counts(deseq2_obj,normalized=T)
65 deseq2_obj_norm.out<-as.data.frame(cbind("OTUID"=rownames(deseq2_obj_norm),deseq2_obj_norm))
66 write.table(deseq2_obj_norm.out,file=options$normalisedResult,col.names=T,row.names=F,quote=F,sep="\t")
67
68
69 ### Normalisation and DE analysis
70 suppressMessages(deseq2_obj_DE<-DESeq(deseq2_obj,test=method,fitType=Type))
71 res = results(deseq2_obj_DE,cooksCutoff = FALSE)
72
73 significant.table <-res[which(res$padj < cutoff),]
74
75 if(nrow(significant.table) == 0){
76 out_message <-"no significant result found!"
77 write(out_message,file=options$result,sep="\t")
78 quit("yes")
79 }
80
81 significant.table <- cbind(as(significant.table,"data.frame"), as(tax_table(AIP_galaxy)[rownames(significant.table),],"matrix"))
82
83 significant.table.out<-as.data.frame(cbind("OTUID"=rownames(significant.table),significant.table))
84
85 write.table(format(significant.table.out, digits=4, scientific=F),file=options$result,col.names=T,row.names=F,quote=F,sep="\t")
86