Mercurial > repos > iuc > raceid_trajectory
view scripts/clusterinspect.R @ 4:3e5bb16abb55 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
author | iuc |
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date | Mon, 12 Aug 2019 13:02:23 -0400 |
parents | ff7cd3c7c1df |
children | 72979cac22b2 |
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#!/usr/bin/env R VERSION = "0.5" 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){ 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 ## - Note: no names in tsne, so we assume it follows the ndata naming sc.tmp@tsne <- sc.tmp@tsne[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, 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){ 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()