annotate scripts/clusterinspect.R @ 7:e93b008c637a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit b461ba94158cf4cc793919470b78bd3eb91312eb"

#!/usr/bin/env R
VERSION <- "0.5"  # nolint

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])

## layout
test <- list()
test$side <- 3
test$line <- 3

do.plotting <- function(sc) { # nolint

    sc_tmp <- sc

    ## If it's a subset, we need to get clever and subset specific parts
    if (!(is.null(plotting.cln) || is.na(plotting.cln))) {
        cellstokeep <- names(sc_tmp@cpart[sc_tmp@cpart %in% plotting.cln])

        ## Subselect partitions for initial and final clusters
        sc_tmp@cpart <- sc_tmp@cpart[cellstokeep]
        sc_tmp@cluster$kpart <- sc_tmp@cluster$kpart[cellstokeep]

        ## Subselect tSNE and FR data
        sc_tmp@tsne <- sc_tmp@tsne[colnames(sc_tmp@ndata) %in% cellstokeep, ]
        sc_tmp@umap <- sc_tmp@umap[colnames(sc_tmp@ndata) %in% cellstokeep, ]
        sc_tmp@fr <- sc_tmp@fr[cellstokeep, ]
    }

    print(plotmap(sc_tmp, final = FALSE, fr = FALSE))
    print(do.call(mtext, c("Initial Clustering tSNE", test)))
    print(plotmap(sc_tmp, final = TRUE, fr = FALSE))
    print(do.call(mtext, c("Final Clustering tSNE", test)))
    print(plotmap(sc_tmp, final = FALSE, um = TRUE))
    print(do.call(mtext, c("Initial Clustering UMAP", test)))
    print(plotmap(sc_tmp, final = TRUE, um = TRUE))
    print(do.call(mtext, c("Final Clustering UMAP", test)))
    print(plotmap(sc_tmp, final = FALSE, fr = TRUE))
    print(do.call(mtext, c("Initial Clustering Fruchterman-Reingold", test)))
    print(plotmap(sc_tmp, final = TRUE, fr = TRUE))
    print(do.call(mtext, c("Final Clustering Fruchterman-Reingold", test)))
}


do.inspect.symbolmap <- function(sc) {  # nolint
    if (!is.null(plotsym.use.typeremoveregex)) {
        plotsym$types <- sub(plotsym.use.typeremoveregex, "",
                             colnames(sc@ndata))

        if (!is.null(plotsym.use.typeremoveregex.subselect)) {
            plotsym$subset <- plotsym$types[grep(
                                          plotsym.use.typeremoveregex.subselect,
                                          plotsym$types)]
        }
    }
    plotsym$fr <- FALSE
    print(do.call(plotsymbolsmap, c(sc, plotsym)))
    print(do.call(mtext, c("Symbols tSNE", test)))
    plotsym$fr <- TRUE
    print(do.call(plotsymbolsmap, c(sc, plotsym)))
    print(do.call(mtext, c("Symbols FR", test)))
}

do.inspect.diffgene <- function(sc) {  # nolint

    getSubNames <- function(lob, sc) {  # nolint
        use_names <- NULL
        if (!is.null(lob$manual)) {
            use_names <- lob$manual
        }
        else if (!is.null(lob$regex)) {
            nm <- colnames(sc@ndata)
            use_names <- nm[grep(lob$regex, nm)]
        }
        else if (!is.null(lob$cln)) {
            use_names <- names(sc@cpart)[sc@cpart %in% lob$cln]
        }
        if (is.null(use_names)) {
            stop("A or B names not given!")
        }
        return(use_names)
    }

    A <- getSubNames(gfdat.A.use, sc) # nolint
    B <- getSubNames(gfdat.B.use, sc) # nolint

    fdat <- getfdata(sc, n = c(A, B))
    dexp <- diffexpnb(fdat, A = A, B = B)
    ## options for diffexpnb are mostly about DESeq, ignore
    plotdiffg$x <- dexp
    print(do.call(plotdiffgenesnb, c(plotdiffg)))
    print(do.call(mtext, c("Diff Genes", test)))
}


do.inspect.genesofinterest <- function(sc) {  # nolint
    if (is.null(plotexp$n)) { ## No title, and one gene? Use gene name
        if (length(plotexp$g) == 1) {
            plotexp$n <- plotexp$g
        } else {
            plotexp$n <- paste(plotexp$g, collapse = ", ")
        }
    }

    title <- paste(":", plotexp$n)
    plotexp$n <- ""

    plotexp$logsc <- FALSE; plotexp$fr <- FALSE
    print(do.call(plotexpmap, c(sc, plotexp)))
    print(do.call(mtext, c(paste("tSNE", title), test)))

    plotexp$logsc <- TRUE; plotexp$fr <- FALSE
    print(do.call(plotexpmap, c(sc, plotexp)))
    print(do.call(mtext, c(paste("tSNE (Log)", title), test)))

    plotexp$logsc <- FALSE; plotexp$fr <- TRUE
    print(do.call(plotexpmap, c(sc, plotexp)))
    print(do.call(mtext, c(paste("FR", title), test)))

    plotexp$logsc <- TRUE; plotexp$fr <- TRUE
    print(do.call(plotexpmap, c(sc, plotexp)))
    print(do.call(mtext, c(paste("FR (Log)", title), test)))

    if (!is.null(plotmarkg$samples)) {
        reg <- plotmarkg$samples
        plotmarkg$samples <- sub("(\\_\\d+)$", "", colnames(sc@ndata))
    }
    print(do.call(plotmarkergenes, c(sc, plotmarkg)))
}

sc <- in.rdat

pdf(out.pdf)
if (perform.plotting) do.plotting(sc)
if (perform.symbolmap) do.inspect.symbolmap(sc)
if (perform.genesofinterest) do.inspect.genesofinterest(sc)
if (perform.diffgene) do.inspect.diffgene(sc)
dev.off()