comparison scripts/trajectoryinspect.R @ 10:2bfd55b87af3 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f

9:2af7c5086a96

VERSION <- "0.2" # nolint

args <- commandArgs(trailingOnly = TRUE)

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

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

        ltr,
        do.call("makeBranchLink", as.list(trjsid.branchcells.ijk))
    )
    write.table(
        head(bra$diffgenes$z, trjsid.numdiffgenes),
        file = out.diffgenes)

    par(mfrow = c(3, 2), cex = 0.5)
    print(do.call(plotmap, c(bra$scl, final = FALSE, fr = FALSE)))
    print(do.call(mtext, c("Initial Clusters (tSNE)", test)))
    print(do.call(plotmap, c(bra$scl, final = TRUE, fr = FALSE)))

    trjfid_getsom$x <- fs
    s1d <- do.call(getsom, c(trjfid_getsom))
    trjfid_procsom$s1d <- s1d
    ps <- do.call(procsom, c(trjfid_procsom))

    y    <- ltr@sc@cpart[n$f]
    fcol <- ltr@sc@fcol

    trjfid_plotheat$xpart <- y
    trjfid_plotheat$xcol <- fcol

    test$side <- 3
    test$line <- 3

    ##Plot average z-score for all modules derived from the SOM:
    trjfid_plotheat$x <- ps$nodes.z
    trjfid_plotheat$ypart <- unique(ps$nodes)
    print(do.call(plotheatmap, c(trjfid_plotheat)))
    print(do.call(mtext, c("Average z-score for all modules derived from SOM",
                           test)))
    ##Plot z-score profile of each gene ordered by SOM modules:
    trjfid_plotheat$x <- ps$all.z
    trjfid_plotheat$ypart <- ps$nodes
    print(do.call(plotheatmap, c(trjfid_plotheat)))
    print(do.call(mtext, c(paste0("z-score profile of each gene",
                                  "ordered by SOM modules"), test)))
    ##Plot normalized expression profile of each gene ordered by SOM modules:
    trjfid_plotheat$x <- ps$all.e
    trjfid_plotheat$ypart <- ps$nodes
    print(do.call(plotheatmap, c(trjfid_plotheat)))
    print(do.call(mtext, c(paste0("Normalized expression profile of each",
                                  "gene ordered by SOM modules"), test)))
    ##Plot binarized expression profile of each gene
    ##(z-score < -1, -1 < z-score < 1, z-score > 1)
    trjfid_plotheat$x <- ps$all.b
    trjfid_plotheat$ypart <- ps$nodes
    print(do.call(plotheatmap, c(trjfid_plotheat)))
    print(do.call(mtext, c("Binarized expression profile of each gene", test)))
    ## This should be written out, and passed back into the tool

10:2bfd55b87af3

VERSION <- "0.2" # nolint

args <- commandArgs(trailingOnly = TRUE)

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

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

        ltr,
        do.call("makeBranchLink", as.list(trjsid.branchcells.ijk))
    )
    write.table(
        head(bra$diffgenes$z, trjsid.numdiffgenes),
        file = out.diffgenes
    )

    par(mfrow = c(3, 2), cex = 0.5)
    print(do.call(plotmap, c(bra$scl, final = FALSE, fr = FALSE)))
    print(do.call(mtext, c("Initial Clusters (tSNE)", test)))
    print(do.call(plotmap, c(bra$scl, final = TRUE, fr = FALSE)))

    trjfid_getsom$x <- fs
    s1d <- do.call(getsom, c(trjfid_getsom))
    trjfid_procsom$s1d <- s1d
    ps <- do.call(procsom, c(trjfid_procsom))

    y <- ltr@sc@cpart[n$f]
    fcol <- ltr@sc@fcol

    trjfid_plotheat$xpart <- y
    trjfid_plotheat$xcol <- fcol

    test$side <- 3
    test$line <- 3

    ## Plot average z-score for all modules derived from the SOM:
    trjfid_plotheat$x <- ps$nodes.z
    trjfid_plotheat$ypart <- unique(ps$nodes)
    print(do.call(plotheatmap, c(trjfid_plotheat)))
    print(do.call(mtext, c(
        "Average z-score for all modules derived from SOM",
        test
    )))
    ## Plot z-score profile of each gene ordered by SOM modules:
    trjfid_plotheat$x <- ps$all.z
    trjfid_plotheat$ypart <- ps$nodes
    print(do.call(plotheatmap, c(trjfid_plotheat)))
    print(do.call(mtext, c(paste0(
        "z-score profile of each gene",
        "ordered by SOM modules"
    ), test)))
    ## Plot normalized expression profile of each gene ordered by SOM modules:
    trjfid_plotheat$x <- ps$all.e
    trjfid_plotheat$ypart <- ps$nodes
    print(do.call(plotheatmap, c(trjfid_plotheat)))
    print(do.call(mtext, c(paste0(
        "Normalized expression profile of each",
        "gene ordered by SOM modules"
    ), test)))
    ## Plot binarized expression profile of each gene
    ## (z-score < -1, -1 < z-score < 1, z-score > 1)
    trjfid_plotheat$x <- ps$all.b
    trjfid_plotheat$ypart <- ps$nodes
    print(do.call(plotheatmap, c(trjfid_plotheat)))
    print(do.call(mtext, c("Binarized expression profile of each gene", test)))
    ## This should be written out, and passed back into the tool