comparison scripts/raceID_kmeans_heatmap.R @ 0:e01c989c7543 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
author iuc
date Sat, 03 Mar 2018 17:34:16 -0500
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-1:000000000000 0:e01c989c7543
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 message("Performing clustering using the following parameters: metric=%s, cln=%.0f, do.gap=%.0f clustnr=%.0f, B.gap=%.0f, SE.method=%s, SE.factor=%.2f, bootnr=%.0f, rseed=%.0f", c_metric, c_cln, dogap, c_clustnr, bgap, semethod, sefactor, c_bootnr, c_rseed)
15
16 sc <- clustexp(
17 sc,
18 metric=c_metric, cln=c_cln, do.gap=dogap, clustnr=c_clustnr,
19 B.gap=bgap, SE.method=semethod, SE.factor=sefactor,
20 bootnr=c_bootnr, rseed=c_rseed
21 )
22
23 message("Plotting images")
24 plotter("plot_gap", plotgap(sc))
25 plotter("plot_jaccard", plotjaccard(sc))
26 plotter("plot_silhouette", plotsilhouette(sc))
27 plotter("plot_clustheatmap", x <- clustheatmap(sc, final=FALSE, hmethod="single"))
28
29
30 message("Finished plots")
31
32 if (generate_final_rdata){
33 message("Saving SC object")
34 saveRDS(sc, output_rdat)
35 }
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