Mercurial > repos > iuc > raceid_inspectclusters
view scripts/clusterinspect.R @ 9:f3eb2291da05 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf
author | iuc |
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date | Wed, 24 Aug 2022 18:11:37 +0000 |
parents | 41f34e925bd5 |
children |
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#!/usr/bin/env R VERSION <- "0.5" # nolint args <- commandArgs(trailingOnly = TRUE) 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()