annotate scripts/raceID_tsne.R @ 0:e01c989c7543 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e

##!/usr/bin/env Rscript

args = commandArgs(trailingOnly=T)

script_dir = args[1]
config_file = args[2]

                                        # Load libs, common functions, source RaceID,
                                        # Galaxy Params, and read input data (sc)
source(paste(script_dir, "common.R", sep="/"))

                                        # Read input data
message("Count matrix with %.0f cells and %.0f genes", dim(sc@fdata)[1], dim(sc@fdata)[2])

sc <- comptsne(sc,rseed = c_rseed)

message("Plotting initial and final tSNEs")

plotter("plot_initial", plottsne(sc,final = F))
plotter("plot_final", plottsne(sc,final = T))

if (gene_sets != "" ){
####all_sets <- strsplit(gene_sets, "+?\\s*__split__\\s*,?")
    all_sets <- strsplit(gene_sets, '\\s*\\+?\\s*_split_\\s*,?')
    print(all_sets)

    for (given in all_sets){
        given <- trimws(given)
        message("Plotting %s", given)
        g <- c(unlist(strsplit(given,'\\s*\\+\\s*')))
        plotter(paste("plot", given, sep="_"), plotexptsne(sc,g, n=given, logsc=T))
    }
}


if (regex_val != ""){
    message("using subcell groups")
    plotter("plot_labels", plotlabelstsne(sc, labels = sub(regex_val, "", names(sc@ndata))))
    plotter("plot_symbols", plotsymbolstsne(sc, types = sub(regex_val, "", names(sc@ndata))))
} else {
    message("using all cell ids")
    plotter("plot_labels", plotlabelstsne(sc, labels = names(sc@ndata)))
    plotter("plot_symbols", plotsymbolstsne(sc, types = names(sc@ndata)))
}

message("Saving SC object")
saveRDS(sc, output_rdat)