comparison scripts/cluster.R @ 4:ee0bbc160cb1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"

3:d4646ce659b4

#!/usr/bin/env R
VERSION = "0.4"

args = commandArgs(trailingOnly = T)

if (length(args) != 1){
     message(paste("VERSION:", VERSION))

    })
    write.table(df, file=out.genelist, sep="\t", quote=F)
}

pdf(out.pdf)

if (use.filtnormconf){
    sc <- do.filter(sc)
    message(paste(" - Source:: genes:",nrow(sc@expdata),", cells:",ncol(sc@expdata)))
    message(paste(" - Filter:: genes:",nrow(getfdata(sc)),", cells:",ncol(getfdata(sc))))
    message(paste("         :: ",
                  sprintf("%.1f", 100 * nrow(getfdata(sc))/nrow(sc@expdata)), "% of genes remain,",
                  sprintf("%.1f", 100 * ncol(getfdata(sc))/ncol(sc@expdata)), "% of cells remain"))
}

if (use.cluster){
    par(mfrow=c(2,2))
    sc <- do.cluster(sc)

    par(mfrow=c(2,2), mar=c(1,1,6,1))
    sc <- do.clustmap(sc)

    mkgenelist(sc)
}

dev.off()

saveRDS(sc, out.rdat)

4:ee0bbc160cb1

#!/usr/bin/env R
VERSION = "0.5"

args = commandArgs(trailingOnly = T)

if (length(args) != 1){
     message(paste("VERSION:", VERSION))

    })
    write.table(df, file=out.genelist, sep="\t", quote=F)
}


writecellassignments <- function(sc){
    dat <- sc@cluster$kpart
    tab <- data.frame(row.names = NULL,
                      cells = names(dat),
                      cluster.initial = dat,
                      cluster.final = sc@cpart,
                      is.outlier = names(dat) %in% sc@out$out)

    write.table(tab, file=out.assignments, sep="\t", quote=F, row.names = F)
}


pdf(out.pdf)

if (use.filtnormconf){
    sc <- do.filter(sc)
    message(paste(" - Source:: genes:",nrow(sc@expdata),", cells:",ncol(sc@expdata)))
    message(paste(" - Filter:: genes:",nrow(getfdata(sc)),", cells:",ncol(getfdata(sc))))
    message(paste("         :: ",
                  sprintf("%.1f", 100 * nrow(getfdata(sc))/nrow(sc@expdata)), "% of genes remain,",
                  sprintf("%.1f", 100 * ncol(getfdata(sc))/ncol(sc@expdata)), "% of cells remain"))
    write.table(as.matrix(sc@ndata), file=out.table, col.names=NA, row.names=T, sep="\t", quote=F)
}

if (use.cluster){
    par(mfrow=c(2,2))
    sc <- do.cluster(sc)

    par(mfrow=c(2,2), mar=c(1,1,6,1))
    sc <- do.clustmap(sc)

    mkgenelist(sc)
    writecellassignments(sc)
}

dev.off()

saveRDS(sc, out.rdat)