annotate scripts/pseudotemporal.R @ 3:4164c0da0a5d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit d94b3b8a4c7cf8c604279eb1eea24d32b3868922

#!/usr/bin/env R
VERSION = "0.1"

args = commandArgs(trailingOnly = T)

if (length(args) != 1){
     message(paste("VERSION:", VERSION))
     stop("Please provide the config file")
}

suppressWarnings(suppressPackageStartupMessages(require(RaceID)))
source(args[1])

test <- list()
test$side = 3
test$line = 3
second <- test
second$cex = 0.5
second$line = 2.5


do.pseudotemp <- function(sc){
    pdf(out.pdf)
    ltr <- Ltree(sc)
    ltr <- compentropy(ltr)
    ltr <- do.call(projcells, c(ltr, pstc.projc))
    ltr <- do.call(projback, c(ltr, pstc.projb))
    ltr <- lineagegraph(ltr)
    ltr <- do.call(comppvalue, c(ltr, pstc.comppval))    
    x <- do.call(compscore, c(ltr, pstc.compscore))
    print(do.call(mtext, c("Compute Score", test)))
    print(do.call(mtext, c("No. of inter-cluster links / Delta median entropy of each cluster / StemID2 score (combination of both)", second)))
    plotdistanceratio(ltr)
    print(do.call(mtext, c("Cell-to-Cell Distance Ratio", test)))
    print(do.call(mtext, c("Original vs High-dimensional Embedded Space", second)))
    do.call(plotgraph, c(ltr, pstc.plotgraph))
    print(do.call(mtext, c("Lineage Trajectories                                                      ", test)))
    print(do.call(mtext, c("Colour = Level of Significance, Width = Link Score                                                                                                          ", second)))
    plotspantree(ltr)
    print(do.call(mtext, c("Minimum Spanning Tree", test)))
    plotprojections(ltr)
    print(do.call(mtext, c("Minimum Spanning Tree", test)))
    print(do.call(mtext, c("Cells Projected onto Links", second)))
    test$side = 4
    test$line = 0
    plotlinkscore(ltr)
    print(do.call(mtext, c("Link Score", test)))
    projenrichment(ltr)
    print(do.call(mtext, c("Enrichment Ratios", test)))
    dev.off()

    return(ltr)
}

ltr <- do.pseudotemp(in.rdat)


saveRDS(ltr, out.rdat)