Mercurial > repos > iuc > raceid_diffgene

comparison scripts/raceID_diffgenes.R @ 0:d6a18fea319f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
author iuc
date Sat, 03 Mar 2018 17:33:01 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:d6a18fea319f
1 #!/usr/bin/env Rscript
2
3 args = commandArgs(trailingOnly=T)
4
5 script_dir = args[1]
6 config_file = args[2]
7
8 # Load libs, common functions, source RaceID,
9 # Galaxy Params, and read input data (sc)
10 source(paste(script_dir, "common.R", sep="/"))
11
12 # Read input data
13 message("Count matrix with %.0f cells and %.0f genes", dim(sc@fdata)[1], dim(sc@fdata)[2])
14
15 cdiff <- clustdiffgenes(sc, pvalue=c_pval)
16
17 if (generate_extable){
18 # differentially expressed genes in cluster
19
20 if (!(dir.exists(outtable_dir))){
21 dir.create(outtable_dir)
22 }
23
24 for ( n in names(cdiff) ){
25 write.table(
26 data.frame(
27 GENEID=rownames(cdiff[[n]]),
28 cdiff[[n]]
29 ),
30 paste(outtable_dir, "/gdiff", "_", n, ".tsv", sep=""), # gdiff_cl.n.tsv
31 row.names=FALSE,
32 col.names=TRUE,
33 sep="\t",
34 quote=FALSE
35 )
36 }
37 }
38
39 if (compare_clusters){
40 clust1 <- c(unlist(lapply(strsplit(clust1, "\\s*,\\s*"), as.integer)))
41 clust2 <- c(unlist(lapply(strsplit(clust2, "\\s*,\\s*"), as.integer)))
42
43 if (length(clust1) == 1){ clust1 <- clust1[[1]] }
44 if (length(clust2) == 1){ clust2 <- clust2[[1]] }
45
46 message("Performing diffgenes with cl1=%s, cl2=%s, mincount=%.0f, gene='%s'", clust1, clust2, mcount, gene_name)
47 d <- diffgenes(sc,cl1 = clust1, cl2 = clust2, mincount = mcount)
48
49 plotter("plot_diffgenes", plotdiffgenes(d,gene= gene_name))
50 }