diff scripts/clusterinspect.R @ 0:9fec5dd8fbb9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/clusterinspect.R	Thu Nov 22 04:45:41 2018 -0500
@@ -0,0 +1,121 @@
+#!/usr/bin/env R
+VERSION = "0.2"
+
+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){
+    print(plotmap(sc, final = FALSE, fr = FALSE))
+    print(do.call(mtext, c("Initial Clustering tSNE", test)))
+    print(plotmap(sc, final = TRUE, fr = FALSE))
+    print(do.call(mtext, c("Final Clustering tSNE", test)))
+    print(plotmap(sc, final = FALSE, fr = TRUE))
+    print(do.call(mtext, c("Initial Clustering Fruchterman-Reingold", test)))
+    print(plotmap(sc, final = TRUE, fr = TRUE))
+    print(do.call(mtext, c("Final Clustering Fruchterman-Reingold", test)))
+}
+
+
+do.inspect.symbolmap <- function(sc){
+    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){
+
+    getSubNames <- function(lob, sc){
+        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)
+    B <- getSubNames(gfdat.B.use, sc)
+
+    fdat <- getfdata(sc, n=c(A,B))
+    dexp <- diffexpnb(fdat, A=A, B=B)
+    ## options for diffexpnb are mostly about DESeq, ignore
+    plotdiffg$x = dexp
+    print(do.call(plotdiffgenesnb, c(plotdiffg)))
+    print(do.call(mtext, c("Diff Genes", test)))
+}
+
+
+do.inspect.genesofinterest <- function(sc){
+    if (is.null(plotexp$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()