Mercurial > repos > iuc > raceid_diffgene

comparison scripts/raceID_tsne.R @ 0:ea8215239735 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
author iuc
date Sat, 03 Mar 2018 17:33:56 -0500
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-1:000000000000 0:ea8215239735
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 sc <- comptsne(sc,rseed = c_rseed)
16
17 message("Plotting initial and final tSNEs")
18
19 plotter("plot_initial", plottsne(sc,final = F))
20 plotter("plot_final", plottsne(sc,final = T))
21
22 if (gene_sets != "" ){
23 ####all_sets <- strsplit(gene_sets, "+?\\s*__split__\\s*,?")
24 all_sets <- strsplit(gene_sets, '\\s*\\+?\\s*_split_\\s*,?')
25 print(all_sets)
26
27 for (given in all_sets){
28 given <- trimws(given)
29 message("Plotting %s", given)
30 g <- c(unlist(strsplit(given,'\\s*\\+\\s*')))
31 plotter(paste("plot", given, sep="_"), plotexptsne(sc,g, n=given, logsc=T))
32 }
33 }
34
35
36 if (regex_val != ""){
37 message("using subcell groups")
38 plotter("plot_labels", plotlabelstsne(sc, labels = sub(regex_val, "", names(sc@ndata))))
39 plotter("plot_symbols", plotsymbolstsne(sc, types = sub(regex_val, "", names(sc@ndata))))
40 } else {
41 message("using all cell ids")
42 plotter("plot_labels", plotlabelstsne(sc, labels = names(sc@ndata)))
43 plotter("plot_symbols", plotsymbolstsne(sc, types = names(sc@ndata)))
44 }
45
46 message("Saving SC object")
47 saveRDS(sc, output_rdat)