Mercurial > repos > iuc > raceid_main

comparison scripts/raceID_outlierdetect.R @ 0:e01c989c7543 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 17:34:16 -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("Detecting outliers using the following parameters: outminc=%.0f, outlg=%.0f, probthr=%.0f outdistquant=%.0f", c_outminc, c_outlg, c_probthr, c_outdistquant)
15
16 sc <- findoutliers(
17 sc, outminc=c_outminc, outlg=c_outlg, probthr=c_probthr,
18 thr=2**-(1:40), outdistquant=c_outdistquant
19 )
20
21 message("Plotting images")
22 plotter("plot_background", plotbackground(sc))
23 plotter("plot_sensitivity", plotsensitivity(sc))
24 plotter("plot_outlierprobs", plotoutlierprobs(sc))
25 plotter("plot_finalheat", y <- clustheatmap(sc,final=TRUE,hmethod="single"))
26
27
28 message("Finished plots")
29
30 message("Generating data tables")
31 x <- data.frame( CELLID=names(sc@cpart), cluster=sc@cpart )
32 write.table(
33 x[order(x$cluster,decreasing=FALSE),], output_table,
34 row.names=FALSE, col.names=TRUE, sep="\t", quote=FALSE
35 )
36
37 if (generate_final_rdata){
38 message("Saving SC object")
39 saveRDS(sc, output_rdat)
40 }
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