| Previous changeset 5:7e014059a88d (2020-01-29) Next changeset 7:c4f39bf4a068 (2021-12-02) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af" |
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modified:
macros.xml macros_cheetah.xml raceid_clustering.xml scripts/cluster.R scripts/clusterinspect.R scripts/pseudotemporal.R scripts/trajectoryinspect.R test-data/intestinal.pdf test-data/intestinal_advanced.filter.pdf test-data/intestinal_advanced.pdf test-data/matrix.filter.geqone.pdf test-data/matrix.filter.pdf test-data/matrix.filter.rdat test-data/matrix2.pdf test-data/matrix2.rdat test-data/out_cluster_default.rdat test-data/out_traject_adv_nondef.pdf test-data/out_traject_default.ltree.rdat test-data/out_traject_default.pdf test-data/out_traject_inspect_allthree.pdf test-data/out_traject_inspect_fateid.pdf test-data/out_traject_inspect_stemid.pdf |
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removed:
test-data/intestinal.genelist test-data/intestinal_advanced.genelist test-data/matrix2.genelist |
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| diff -r 7e014059a88d -r a4b734cd253b macros.xml --- a/macros.xml Wed Jan 29 17:16:36 2020 -0500 +++ b/macros.xml Thu Apr 15 18:58:21 2021 +0000 |
| [ |
| @@ -25,8 +25,8 @@ return(unlist(strsplit(string,","))) } </token> - <token name="@VERSION_RACEID@">3</token> - <token name="@VERSION_WRAPPER@">1</token> + <token name="@VERSION_RACEID@">0.2.3</token> + <token name="@VERSION_WRAPPER@">0</token> <macro name="version_command_config" token_prog="temp" token_cheetah="temp2" token_out="2> '$outlog'"> <version_command><![CDATA[ @@ -47,8 +47,8 @@ <macro name="requirements" > <requirements> - <requirement type="package" version="0.1.1">r-raceid</requirement> - <requirement type="package" version="1.6.2">bioconductor-scran</requirement> + <requirement type="package" version="@VERSION_RACEID@" >r-raceid</requirement> + <!-- <requirement type="package" version="1.6.2">bioconductor-scran</requirement> --> </requirements> </macro> <macro name="yesno_checkedno" > |
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| diff -r 7e014059a88d -r a4b734cd253b macros_cheetah.xml --- a/macros_cheetah.xml Wed Jan 29 17:16:36 2020 -0500 +++ b/macros_cheetah.xml Thu Apr 15 18:58:21 2021 +0000 |
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| @@ -127,15 +127,19 @@ outlier.rfcorrect\$nbfactor = as.integer( '$outlier.use.nbfactor' ) #end if +cluster.compumap = formals(compumap) cluster.comptsne = formals(comptsne) cluster.compfr = formals(compfr) cluster.comptsne\$perplexity = as.integer( '$tsne.perplexity' ) cluster.compfr\$knn = as.integer( '$tsne.knn' ) +cluster.compumap\$n_neighbors = as.integer( '$tsne.umap_nn' ) #if str($tsne.use.def) == "no": cluster.comptsne\$initial_cmd = as.logical( '$tsne.use.initial_cmd' ) cluster.comptsne\$rseed = as.integer( '$tsne.use.rseed_tsne' ) cluster.compfr\$rseed = as.integer( '$tsne.use.rseed_fr' ) +cluster.compumap\$n_epochs = as.integer( '$tsne.use.umap_epochs' ) +cluster.compumap\$min_dist = as.numeric( '$tsne.use.umap_min_dist' ) #end if genelist.tablelim = as.integer( '$extra.tablelim' ) @@ -227,6 +231,7 @@ perform.diffgene = TRUE plotdiffg\$Aname = '$diffgtest.set_a.name_set' plotdiffg\$Bname = '$diffgtest.set_b.name_set' +plotdiffg\$... = NULL gfdat.A.use = list() gfdat.B.use = list() @@ -294,7 +299,7 @@ pstc.plotgraph\$showCells = as.logical( '$plotgraph.showcells' ) pstc.plotgraph\$scthr = as.numeric( '$plotgraph.scthr' ) #if str($plotgraph.use.def) == "no": -pstc.plotgraph\$showTsne = as.logical( '$plotgraph.use.showtsne' ) +##pstc.plotgraph\$showTsne = as.logical( '$plotgraph.use.showtsne' ) pstc.plotgraph\$tp = as.numeric( '$plotgraph.use.tp' ) #end if |
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| diff -r 7e014059a88d -r a4b734cd253b raceid_clustering.xml --- a/raceid_clustering.xml Wed Jan 29 17:16:36 2020 -0500 +++ b/raceid_clustering.xml Thu Apr 15 18:58:21 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="raceid_clustering" name="Clustering using RaceID" version="@VERSION_RACEID@.@VERSION_WRAPPER@" > +<tool id="raceid_clustering" name="Clustering using RaceID" version="@VERSION_RACEID@+galaxy@VERSION_WRAPPER@" > <description>performs clustering, outlier detection, dimensional reduction</description> <macros> <import>macros.xml</import> @@ -52,17 +52,22 @@ <param name="rfseed" type="integer" value="12345" label="Random Seed" /> </expand> </section> - <section name="tsne" title="tSNE and FR" expanded="true" > + <section name="tsne" title="tSNE, FR and UMAP" expanded="true" > <!-- CompTSNE --> <param name="perplexity" type="integer" min="0" value="30" label="Perplexity" help="Perplexity of the t-SNE map" /> <!-- CompFR --> - <param name="knn" type="integer" min="0" value="10" label="KNN" help="Number of nearest neighbours used for the inference of the Fruchterman-Rheingold layout" /> + <param name="knn" type="integer" min="1" value="10" label="KNN" help="Number of nearest neighbours used for the inference of the Fruchterman-Rheingold layout" /> + <!-- CompUMAP --> + <param name="umap_nn" type="integer" min="1" value="15" label="N Neighbours" help="Number of nearest neighbours used for the UMAP connectivity" /> <expand macro="use_defaults_no" > <!-- CompTSNE --> <param name="initial_cmd" type="boolean" checked="true" label="tSNE map initialised by classical multidimensional scaling" /> <param name="rseed_tsne" type="integer" value="15555" label="Random Seed (tSNE)" /> <!-- CompFR --> <param name="rseed_fr" type="integer" min="0" value="15555" label="Random Seed (FR)" /> + <!-- CompUMAP --> + <param name="umap_epochs" type="integer" min="1" value="200" label="Number Epochs (UMAP)" /> + <param name="umap_min_dist" type="float" min="0" value="0.1" label="Min Dist (UMAP)" /> </expand> </section> <section name="extra" title="Extra Parameters" expanded="false" > @@ -84,9 +89,14 @@ <tests> <test> <param name="inputrds" value="matrix.filter.rdat" /> - <output name="outgenelist" value="matrix2.genelist" compare="re_match"/> - <output name="outrdat" value="matrix2.rdat" compare="sim_size" delta="15" /> - <output name="outpdf" value="matrix2.pdf" compare="sim_size" delta="10" /> + <output name="outgenelist" > + <assert_contents> + <has_line_matching expression=".*ENSDARG00000108379\s+1.*" /> + <has_line_matching expression=".*ENSDARG00000027310\s+8.*" /> + </assert_contents> + </output> + <output name="outrdat" value="matrix2.rdat" compare="sim_size" delta="500" /> + <output name="outpdf" value="matrix2.pdf" compare="sim_size" delta="100" /> <output name="outassignments" > <assert_contents> <has_line_matching expression="P1_B1_ATCCAC\s1\s1\sFALSE" /> @@ -127,7 +137,12 @@ <param name="rfseed_fr" value="15555" /> </expand> </section> - <output name="outgenelist" value="intestinal.genelist" compare="re_match"/> + <output name="outgenelist" > + <assert_contents> + <has_line_matching expression=".*ENSDARG00000108379\s+1.*" /> + <has_line_matching expression=".*ENSDARG00000027310\s+8.*" /> + </assert_contents> + </output> <output name="outpdf" value="intestinal.pdf" compare="sim_size" delta="50" /> </test> <test> @@ -168,7 +183,12 @@ <param name="rfseed_fr" value="15555" /> </expand> </section> - <output name="outgenelist" value="intestinal_advanced.genelist" compare="re_match"/> + <output name="outgenelist" > + <assert_contents> + <has_line_matching expression=".*ENSDARG00000107138\s+1.*" /> + <has_line_matching expression=".*ENSDARG00000016138\s+10.*" /> + </assert_contents> + </output> <output name="outpdf" value="intestinal_advanced.pdf" compare="sim_size" delta="150" /> </test> </tests> |
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| diff -r 7e014059a88d -r a4b734cd253b scripts/cluster.R --- a/scripts/cluster.R Wed Jan 29 17:16:36 2020 -0500 +++ b/scripts/cluster.R Thu Apr 15 18:58:21 2021 +0000 |
| [ |
| b'@@ -1,91 +1,77 @@\n #!/usr/bin/env R\n-VERSION = "0.5"\n+VERSION <- "0.5" # nolint\n \n-args = commandArgs(trailingOnly = T)\n+args <- commandArgs(trailingOnly = T)\n \n-if (length(args) != 1){\n+if (length(args) != 1) {\n message(paste("VERSION:", VERSION))\n stop("Please provide the config file")\n }\n \n suppressWarnings(suppressPackageStartupMessages(require(RaceID)))\n-suppressWarnings(suppressPackageStartupMessages(require(scran)))\n+## suppressWarnings(suppressPackageStartupMessages(require(scran))) # nolint\n source(args[1])\n \n \n-do.filter <- function(sc){\n- if (!is.null(filt.lbatch.regexes)){\n+do.filter <- function(sc) { # nolint\n+ if (!is.null(filt.lbatch.regexes)) {\n lar <- filt.lbatch.regexes\n nn <- colnames(sc@expdata)\n- filt$LBatch <- lapply(1:length(lar), function(m){ return( nn[grep(lar[[m]], nn)] ) })\n+ filt$LBatch <- lapply(1:length(lar), function(m) { # nolint\n+ return(nn[grep(lar[[m]], nn)])})\n }\n \n sc <- do.call(filterdata, c(sc, filt))\n \n ## Get histogram metrics for library size and number of features\n- raw.lib <- log10(colSums(as.matrix(sc@expdata)))\n- raw.feat <- log10(colSums(as.matrix(sc@expdata)>0))\n- filt.lib <- log10(colSums(getfdata(sc)))\n- filt.feat <- log10(colSums(getfdata(sc)>0))\n+ raw_lib <- log10(colSums(as.matrix(sc@expdata)))\n+ raw_feat <- log10(colSums(as.matrix(sc@expdata) > 0))\n+ filt_lib <- log10(colSums(as.matrix(getfdata(sc))))\n+ filt_feat <- log10(colSums(as.matrix(getfdata(sc) > 0)))\n \n- if (filt.geqone){\n- filt.feat <- log10(colSums(getfdata(sc)>=1))\n+ if (filt.geqone) {\n+ filt_feat <- log10(colSums(as.matrix(getfdata(sc) >= 1))) # nolint\n }\n \n br <- 50\n- ## Determine limits on plots based on the unfiltered data\n- ## (doesn\'t work, R rejects limits and norm data is too different to compare to exp data\n- ## so let them keep their own ranges)\n-\n- ## betterrange <- function(floatval){\n- ## return(10 * (floor(floatval / 10) + 1))\n- ## }\n-\n- ## tmp.lib <- hist(raw.lib, breaks=br, plot=F)\n- ## tmp.feat <- hist(raw.feat, breaks=br, plot=F)\n-\n- ## lib.y_lim <- c(0,betterrange(max(tmp.lib$counts)))\n- ## lib.x_lim <- c(0,betterrange(max(tmp.lib$breaks)))\n-\n- ## feat.y_lim <- c(0,betterrange(max(tmp.feat$counts)))\n- ## feat.x_lim <- c(0,betterrange(max(tmp.feat$breaks)))\n-\n- par(mfrow=c(2,2))\n- print(hist(raw.lib, breaks=br, main="RawData Log10 LibSize")) # , xlim=lib.x_lim, ylim=lib.y_lim)\n- print(hist(raw.feat, breaks=br, main="RawData Log10 NumFeat")) #, xlim=feat.x_lim, ylim=feat.y_lim)\n- print(hist(filt.lib, breaks=br, main="FiltData Log10 LibSize")) # , xlim=lib.x_lim, ylim=lib.y_lim)\n- tmp <- hist(filt.feat, breaks=br, main="FiltData Log10 NumFeat") # , xlim=feat.x_lim, ylim=feat.y_lim)\n+ par(mfrow = c(2, 2))\n+ print(hist(raw_lib, breaks = br, main = "RawData Log10 LibSize"))\n+ print(hist(raw_feat, breaks = br, main = "RawData Log10 NumFeat"))\n+ print(hist(filt_lib, breaks = br, main = "FiltData Log10 LibSize"))\n+ tmp <- hist(filt_feat, breaks = br, main = "FiltData Log10 NumFeat")\n print(tmp)\n ## required, for extracting midpoint\n- unq <- unique(filt.feat)\n- if (length(unq) == 1){\n- abline(v=unq, col="red", lw=2)\n- text(tmp$mids, table(filt.feat)[[1]] - 100, pos=1, paste(10^unq, "\\nFeatures\\nin remaining\\nCells", sep=""), cex=0.8)\n+ unq <- unique(filt_feat)\n+ if (length(unq) == 1) {\n+ abline(v = unq, col = "red", lw = 2)\n+ text(tmp$mids, table(filt_feat)[[1]] - 100, pos = 1,\n+ paste(10^unq, "\\nFeatures\\nin remaining\\nCells",\n+ sep = ""), cex = 0.8)\n }\n \n- if (filt.use.ccorrect){\n- par(mfrow=c(2,2))\n+ if (filt.use.ccorrect) {\n+ par(mfrow = c(2, 2))\n sc <- do.call(CCcorrect, c(sc, filt.ccc))\n- print(plotdimsat(sc, change=T))\n- print(plotdimsat(sc, change=F))\n+ print(plotdimsat(sc, '..b' test <- list()\n- test$side = 3\n- test$line = 0 #1 #3\n- test$cex = 0.8\n+ test$side <- 4\n+ test$line <- -2\n+ test$cex <- 0.8\n \n df <- c()\n options(cex = 1)\n- lapply(unique(sc@cpart), function(n){\n- dg <- clustdiffgenes(sc, cl=n, pvalue=genelist.pvalue)\n+ plot.new()\n+ lapply(unique(sc@cpart), function(n) {\n+ dg <- clustdiffgenes(sc, cl = n, pvalue = genelist.pvalue)$dg\n \n- dg.goi <- dg[dg$fc > genelist.foldchange,]\n- dg.goi.table <- head(dg.goi, genelist.tablelim)\n- df <<- rbind(df, cbind(n, dg.goi.table))\n+ dg_goi <- dg[dg$fc > genelist.foldchange, ]\n+ dg_goi_table <- head(dg_goi, genelist.tablelim)\n+ df <<- rbind(df, cbind(n, dg_goi_table))\n \n- goi <- head(rownames(dg.goi.table), genelist.plotlim)\n+ goi <- head(rownames(dg_goi_table), genelist.plotlim)\n+\n print(plotmarkergenes(sc, goi))\n- buffer <- paste(rep("", 36), collapse=" ")\n- print(do.call(mtext, c(paste(buffer, "Cluster ",n), test))) ## spacing is a hack\n- test$line=-1\n- print(do.call(mtext, c(paste(buffer, "Sig. Genes"), test))) ## spacing is a hack\n- test$line=-2\n- print(do.call(mtext, c(paste(buffer, "(fc > ", genelist.foldchange,")"), test))) ## spacing is a hack\n-\n+ buffer <- paste(rep("", 36), collapse = " ")\n+ print(do.call(mtext, c(paste(buffer, "Cluster ", n), test)))\n+ test$line <- -1\n+ print(do.call(mtext, c(paste(buffer, "Sig. Genes"), test)))\n+ test$line <- 0\n+ print(do.call(mtext, c(paste(buffer, "(fc > ",\n+ genelist.foldchange, ")"), test)))\n })\n- write.table(df, file=out.genelist, sep="\\t", quote=F)\n+ write.table(df, file = out.genelist, sep = "\\t", quote = F)\n }\n \n \n-writecellassignments <- function(sc){\n+writecellassignments <- function(sc) {\n dat <- sc@cluster$kpart\n tab <- data.frame(row.names = NULL,\n cells = names(dat),\n@@ -148,30 +137,38 @@\n cluster.final = sc@cpart,\n is.outlier = names(dat) %in% sc@out$out)\n \n- write.table(tab, file=out.assignments, sep="\\t", quote=F, row.names = F)\n+ write.table(tab, file = out.assignments, sep = "\\t",\n+ quote = F, row.names = F)\n }\n \n \n pdf(out.pdf)\n \n-if (use.filtnormconf){\n+if (use.filtnormconf) {\n sc <- do.filter(sc)\n- message(paste(" - Source:: genes:",nrow(sc@expdata),", cells:",ncol(sc@expdata)))\n- message(paste(" - Filter:: genes:",nrow(getfdata(sc)),", cells:",ncol(getfdata(sc))))\n+ message(paste(" - Source:: genes:", nrow(sc@expdata),\n+ ", cells:", ncol(sc@expdata)))\n+ message(paste(" - Filter:: genes:", nrow(as.matrix(getfdata(sc))),\n+ ", cells:", ncol(as.matrix(getfdata(sc)))))\n message(paste(" :: ",\n- sprintf("%.1f", 100 * nrow(getfdata(sc))/nrow(sc@expdata)), "% of genes remain,",\n- sprintf("%.1f", 100 * ncol(getfdata(sc))/ncol(sc@expdata)), "% of cells remain"))\n- write.table(as.matrix(sc@ndata), file=out.table, col.names=NA, row.names=T, sep="\\t", quote=F)\n+ sprintf("%.1f", 100 * nrow(as.matrix(\n+ getfdata(sc))) / nrow(sc@expdata)),\n+ "% of genes remain,",\n+ sprintf("%.1f", 100 * ncol(as.matrix(\n+ getfdata(sc))) / ncol(sc@expdata)),\n+ "% of cells remain"))\n+ write.table(as.matrix(sc@ndata), file = out.table, col.names = NA,\n+ row.names = T, sep = "\\t", quote = F)\n }\n \n-if (use.cluster){\n- par(mfrow=c(2,2))\n+if (use.cluster) {\n+ par(mfrow = c(2, 2))\n sc <- do.cluster(sc)\n \n- par(mfrow=c(2,2))\n+ par(mfrow = c(2, 2))\n sc <- do.outlier(sc)\n \n- par(mfrow=c(2,2), mar=c(1,1,6,1))\n+ par(mfrow = c(2, 2), mar = c(1, 1, 6, 1))\n sc <- do.clustmap(sc)\n \n mkgenelist(sc)\n' |
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| diff -r 7e014059a88d -r a4b734cd253b scripts/clusterinspect.R --- a/scripts/clusterinspect.R Wed Jan 29 17:16:36 2020 -0500 +++ b/scripts/clusterinspect.R Thu Apr 15 18:58:21 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ #!/usr/bin/env R -VERSION = "0.5" +VERSION <- "0.5" # nolint -args = commandArgs(trailingOnly = T) +args <- commandArgs(trailingOnly = T) -if (length(args) != 1){ +if (length(args) != 1) { message(paste("VERSION:", VERSION)) stop("Please provide the config file") } @@ -13,117 +13,124 @@ ## layout test <- list() -test$side = 3 -test$line = 3 +test$side <- 3 +test$line <- 3 -do.plotting <- function(sc){ +do.plotting <- function(sc) { # nolint - sc.tmp <- sc + sc_tmp <- sc ## If it's a subset, we need to get clever and subset specific parts - if (!(is.null(plotting.cln) || is.na(plotting.cln))){ - cellstokeep <- names(sc.tmp@cpart[sc.tmp@cpart %in% plotting.cln]) + if (!(is.null(plotting.cln) || is.na(plotting.cln))) { + cellstokeep <- names(sc_tmp@cpart[sc_tmp@cpart %in% plotting.cln]) ## Subselect partitions for initial and final clusters - sc.tmp@cpart <- sc.tmp@cpart[cellstokeep] - sc.tmp@cluster$kpart <- sc.tmp@cluster$kpart[cellstokeep] + sc_tmp@cpart <- sc_tmp@cpart[cellstokeep] + sc_tmp@cluster$kpart <- sc_tmp@cluster$kpart[cellstokeep] ## Subselect tSNE and FR data - ## - Note: no names in tsne, so we assume it follows the ndata naming - sc.tmp@tsne <- sc.tmp@tsne[colnames(sc.tmp@ndata) %in% cellstokeep,] - sc.tmp@fr <- sc.tmp@fr[cellstokeep,] + sc_tmp@tsne <- sc_tmp@tsne[colnames(sc_tmp@ndata) %in% cellstokeep, ] + sc_tmp@umap <- sc_tmp@umap[colnames(sc_tmp@ndata) %in% cellstokeep, ] + sc_tmp@fr <- sc_tmp@fr[cellstokeep, ] } - print(plotmap(sc.tmp, final = FALSE, fr = FALSE)) + print(plotmap(sc_tmp, final = FALSE, fr = FALSE)) print(do.call(mtext, c("Initial Clustering tSNE", test))) - print(plotmap(sc.tmp, final = TRUE, fr = FALSE)) + print(plotmap(sc_tmp, final = TRUE, fr = FALSE)) print(do.call(mtext, c("Final Clustering tSNE", test))) - print(plotmap(sc.tmp, final = FALSE, fr = TRUE)) + print(plotmap(sc_tmp, final = FALSE, um = TRUE)) + print(do.call(mtext, c("Initial Clustering UMAP", test))) + print(plotmap(sc_tmp, final = TRUE, um = TRUE)) + print(do.call(mtext, c("Final Clustering UMAP", test))) + print(plotmap(sc_tmp, final = FALSE, fr = TRUE)) print(do.call(mtext, c("Initial Clustering Fruchterman-Reingold", test))) - print(plotmap(sc.tmp, final = TRUE, fr = TRUE)) + print(plotmap(sc_tmp, final = TRUE, fr = TRUE)) print(do.call(mtext, c("Final Clustering Fruchterman-Reingold", test))) } -do.inspect.symbolmap <- function(sc){ - if (!is.null(plotsym.use.typeremoveregex)){ - plotsym$types = sub(plotsym.use.typeremoveregex, "", colnames(sc@ndata)) +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)] + if (!is.null(plotsym.use.typeremoveregex.subselect)) { + plotsym$subset <- plotsym$types[grep( + plotsym.use.typeremoveregex.subselect, + plotsym$types)] } } - plotsym$fr = FALSE + plotsym$fr <- FALSE print(do.call(plotsymbolsmap, c(sc, plotsym))) print(do.call(mtext, c("Symbols tSNE", test))) - plotsym$fr = TRUE + plotsym$fr <- TRUE print(do.call(plotsymbolsmap, c(sc, plotsym))) print(do.call(mtext, c("Symbols FR", test))) } -do.inspect.diffgene <- function(sc){ +do.inspect.diffgene <- function(sc) { # nolint - getSubNames <- function(lob, sc){ - use.names <- NULL - if (!is.null(lob$manual)){ - use.names <- lob$manual + getSubNames <- function(lob, sc) { # nolint + use_names <- NULL + if (!is.null(lob$manual)) { + use_names <- lob$manual } - else if (!is.null(lob$regex)){ + else if (!is.null(lob$regex)) { nm <- colnames(sc@ndata) - use.names <- nm[grep(lob$regex, nm)] + use_names <- nm[grep(lob$regex, nm)] } - else if (!is.null(lob$cln)){ - use.names <- names(sc@cpart)[sc@cpart %in% lob$cln] + else if (!is.null(lob$cln)) { + use_names <- names(sc@cpart)[sc@cpart %in% lob$cln] } - if (is.null(use.names)){ + if (is.null(use_names)) { stop("A or B names not given!") } - return(use.names) + return(use_names) } - A <- getSubNames(gfdat.A.use, sc) - B <- getSubNames(gfdat.B.use, sc) + A <- getSubNames(gfdat.A.use, sc) # nolint + B <- getSubNames(gfdat.B.use, sc) # nolint - fdat <- getfdata(sc, n=c(A,B)) - dexp <- diffexpnb(fdat, A=A, B=B) + fdat <- getfdata(sc, n = c(A, B)) + dexp <- diffexpnb(fdat, A = A, B = B) ## options for diffexpnb are mostly about DESeq, ignore - plotdiffg$x = dexp + 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$g) == 1){ +do.inspect.genesofinterest <- function(sc) { # nolint + if (is.null(plotexp$n)) { ## No title, and one gene? Use gene name + if (length(plotexp$g) == 1) { plotexp$n <- plotexp$g } else { - plotexp$n <- paste(plotexp$g, collapse=", ") + plotexp$n <- paste(plotexp$g, collapse = ", ") } } title <- paste(":", plotexp$n) plotexp$n <- "" - plotexp$logsc=FALSE; plotexp$fr = FALSE + plotexp$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$fr = FALSE + plotexp$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$fr = TRUE + plotexp$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$fr = TRUE + plotexp$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)){ + if (!is.null(plotmarkg$samples)) { reg <- plotmarkg$samples - plotmarkg$samples <- sub("(\\_\\d+)$","", colnames(sc@ndata)) + plotmarkg$samples <- sub("(\\_\\d+)$", "", colnames(sc@ndata)) } print(do.call(plotmarkergenes, c(sc, plotmarkg))) } |
| b |
| diff -r 7e014059a88d -r a4b734cd253b scripts/pseudotemporal.R --- a/scripts/pseudotemporal.R Wed Jan 29 17:16:36 2020 -0500 +++ b/scripts/pseudotemporal.R Thu Apr 15 18:58:21 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ #!/usr/bin/env R -VERSION = "0.1" +VERSION <- "0.1" # nolint -args = commandArgs(trailingOnly = T) +args <- commandArgs(trailingOnly = T) # nolint -if (length(args) != 1){ +if (length(args) != 1) { message(paste("VERSION:", VERSION)) stop("Please provide the config file") } @@ -12,37 +12,44 @@ source(args[1]) test <- list() -test$side = 3 -test$line = 3 +test$side <- 3 +test$line <- 3 second <- test -second$cex = 0.5 -second$line = 2.5 +second$cex <- 0.5 +second$line <- 2.5 -do.pseudotemp <- function(sc){ +do.pseudotemp <- function(sc) { # nolint pdf(out.pdf) ltr <- Ltree(sc) ltr <- compentropy(ltr) ltr <- do.call(projcells, c(ltr, pstc.projc)) ltr <- do.call(projback, c(ltr, pstc.projb)) ltr <- lineagegraph(ltr) - ltr <- do.call(comppvalue, c(ltr, pstc.comppval)) + ltr <- do.call(comppvalue, c(ltr, pstc.comppval)) x <- do.call(compscore, c(ltr, pstc.compscore)) print(do.call(mtext, c("Compute Score", test))) - print(do.call(mtext, c("No. of inter-cluster links / Delta median entropy of each cluster / StemID2 score (combination of both)", second))) + print(do.call(mtext, c(paste0("No. of inter-cluster links / ", + "Delta median entropy of each cluster / ", + "StemID2 score (combination of both)"), + second))) plotdistanceratio(ltr) print(do.call(mtext, c("Cell-to-Cell Distance Ratio", test))) - print(do.call(mtext, c("Original vs High-dimensional Embedded Space", second))) + print(do.call(mtext, c("Original vs High-dimensional Embedded Space", + second))) do.call(plotgraph, c(ltr, pstc.plotgraph)) - print(do.call(mtext, c("Lineage Trajectories ", test))) - print(do.call(mtext, c("Colour = Level of Significance, Width = Link Score ", second))) + print(do.call(mtext, c(paste0(c("Lineage Trajectories", rep(" ", 54)), + collapse = ""), test))) + print(do.call(mtext, c(paste0(c(paste0("Colour = Level of Significance, ", + "Width = Link Score"), + rep(" ", 106)), collapse = ""), second))) plotspantree(ltr) print(do.call(mtext, c("Minimum Spanning Tree", test))) - plotprojections(ltr) + plotspantree(ltr, projections = TRUE) print(do.call(mtext, c("Minimum Spanning Tree", test))) print(do.call(mtext, c("Cells Projected onto Links", second))) - test$side = 4 - test$line = 0 + test$side <- 4 + test$line <- 0 plotlinkscore(ltr) print(do.call(mtext, c("Link Score", test))) projenrichment(ltr) |
| b |
| diff -r 7e014059a88d -r a4b734cd253b scripts/trajectoryinspect.R --- a/scripts/trajectoryinspect.R Wed Jan 29 17:16:36 2020 -0500 +++ b/scripts/trajectoryinspect.R Thu Apr 15 18:58:21 2021 +0000 |
| [ |
| @@ -1,9 +1,9 @@ #!/usr/bin/env R -VERSION = "0.2" +VERSION <- "0.2" # nolint -args = commandArgs(trailingOnly = T) +args <- commandArgs(trailingOnly = T) -if (length(args) != 1){ +if (length(args) != 1) { message(paste("VERSION:", VERSION)) stop("Please provide the config file") } @@ -13,17 +13,17 @@ source(args[1]) test <- list() -test$side = 3 -test$line = 2.5 +test$side <- 3 +test$line <- 2.5 second <- test -second$cex = 0.5 -second$line = 2.5 +second$cex <- 0.5 +second$line <- 2.5 -do.trajectoryinspection.stemID <- function(ltr){ - makeBranchLink <- function(i,j,k){ - ingoing <- paste(sort(c(i,j)), collapse=".") - outgoing <- paste(sort(c(j,k)), collapse=".") - messed <- sort(c(ingoing,outgoing)) +do.trajectoryinspection.stemID <- function(ltr) { # nolint + makeBranchLink <- function(i, j, k) { # nolint + ingoing <- paste(sort(c(i, j)), collapse = ".") + outgoing <- paste(sort(c(j, k)), collapse = ".") + messed <- sort(c(ingoing, outgoing)) return(list(messed[[1]], messed[[2]])) } @@ -34,88 +34,99 @@ ) write.table( head(bra$diffgenes$z, trjsid.numdiffgenes), - file=out.diffgenes) + file = out.diffgenes) - par(mfrow = c(2,2), cex=0.5) - print(do.call(plotmap, c(bra$scl, final=FALSE, fr=FALSE))) + par(mfrow = c(3, 2), cex = 0.5) + print(do.call(plotmap, c(bra$scl, final = FALSE, fr = FALSE))) print(do.call(mtext, c("Initial Clusters (tSNE)", test))) - print(do.call(plotmap, c(bra$scl, final=TRUE, fr=FALSE))) + print(do.call(plotmap, c(bra$scl, final = TRUE, fr = FALSE))) print(do.call(mtext, c("Final Clusters (tSNE)", test))) - print(do.call(plotmap, c(bra$scl, final=FALSE, fr=TRUE))) + print(do.call(plotmap, c(bra$scl, final = FALSE, um = TRUE))) + print(do.call(mtext, c("Initial Clusters (UMAP)", test))) + print(do.call(plotmap, c(bra$scl, final = TRUE, um = TRUE))) + print(do.call(mtext, c("Final Clusters (UMAP)", test))) + print(do.call(plotmap, c(bra$scl, final = FALSE, fr = TRUE))) print(do.call(mtext, c("Initial Clusters (F-R)", test))) - print(do.call(plotmap, c(bra$scl, final=TRUE, fr=TRUE))) + print(do.call(plotmap, c(bra$scl, final = TRUE, fr = TRUE))) print(do.call(mtext, c("Final Clusters (F-R)", test))) } -do.trajectoryinspection.fateID <- function(ltr){ +do.trajectoryinspection.fateID <- function(ltr) { # nolint n <- do.call(cellsfromtree, c(ltr, trjfid.cellsfrom)) x <- getfdata(ltr@sc) - trjfid.filterset$x = x - trjfid.filterset$n = n$f + trjfid.filterset$x <- x + trjfid.filterset$n <- n$f fs <- do.call(filterset, c(trjfid.filterset)) - trjfid.getsom$x = fs + trjfid.getsom$x <- fs s1d <- do.call(getsom, c(trjfid.getsom)) - trjfid.procsom$s1d = s1d + trjfid.procsom$s1d <- s1d ps <- do.call(procsom, c(trjfid.procsom)) y <- ltr@sc@cpart[n$f] fcol <- ltr@sc@fcol - trjfid.plotheat$xpart = y - trjfid.plotheat$xcol = fcol + trjfid.plotheat$xpart <- y + trjfid.plotheat$xcol <- fcol + + test$side <- 3 + test$line <- 3 ##Plot average z-score for all modules derived from the SOM: - trjfid.plotheat$x = ps$nodes.z - trjfid.plotheat$ypart = unique(ps$nodes) + trjfid.plotheat$x <- ps$nodes.z + trjfid.plotheat$ypart <- unique(ps$nodes) print(do.call(plotheatmap, c(trjfid.plotheat))) - print(do.call(mtext, c("Average z-score for all modules derived from SOM", test))) + print(do.call(mtext, c("Average z-score for all modules derived from SOM", + test))) ##Plot z-score profile of each gene ordered by SOM modules: - trjfid.plotheat$x = ps$all.z - trjfid.plotheat$ypart = ps$nodes + trjfid.plotheat$x <- ps$all.z + trjfid.plotheat$ypart <- ps$nodes print(do.call(plotheatmap, c(trjfid.plotheat))) - print(do.call(mtext, c("z-score profile of each gene ordered by SOM modules", test))) + print(do.call(mtext, c(paste0("z-score profile of each gene", + "ordered by SOM modules"), test))) ##Plot normalized expression profile of each gene ordered by SOM modules: - trjfid.plotheat$x = ps$all.e - trjfid.plotheat$ypart = ps$nodes + trjfid.plotheat$x <- ps$all.e + trjfid.plotheat$ypart <- ps$nodes print(do.call(plotheatmap, c(trjfid.plotheat))) - print(do.call(mtext, c("Normalized expression profile of each gene ordered by SOM modules", test))) - ##Plot binarized expression profile of each gene (z-score < -1, -1 < z-score < 1, z-score > 1): - trjfid.plotheat$x = ps$all.b - trjfid.plotheat$ypart = ps$nodes + print(do.call(mtext, c(paste0("Normalized expression profile of each", + "gene ordered by SOM modules"), test))) + ##Plot binarized expression profile of each gene + ##(z-score < -1, -1 < z-score < 1, z-score > 1) + trjfid.plotheat$x <- ps$all.b + trjfid.plotheat$ypart <- ps$nodes print(do.call(plotheatmap, c(trjfid.plotheat))) print(do.call(mtext, c("Binarized expression profile of each gene", test))) ## This should be written out, and passed back into the tool ## to perform sominspect - return(list(fs=fs,ps=ps,y=y,fcol=fcol,nf=n$f)) + return(list(fs = fs, ps = ps, y = y, fcol = fcol, nf = n$f)) } -do.trajectoryinspection.fateID.sominspect <- function(domo){ +do.trajectoryinspection.fateID.sominspect <- function(domo) { # nolint g <- trjfidsomi.use.genes - if (class(g) == "numeric"){ + if (class(g) == "numeric") { g <- names(ps$nodes)[ps$nodes %in% g] } - typ = NULL - if (!is.null(trjfidsomi.use.types)){ - typ = sub(trjfidsomi.use.types,"", domo$nf) + typ <- NULL + if (!is.null(trjfidsomi.use.types)) { + typ <- sub(trjfidsomi.use.types, "", domo$nf) } - trjfidsomi$x = domo$fs - trjfidsomi$y = domo$y - trjfidsomi$g = g - trjfidsomi$n = domo$nf - trjfidsomi$col = domo$fcol - trjfidsomi$types = typ + trjfidsomi$x <- domo$fs + trjfidsomi$y <- domo$y + trjfidsomi$g <- g + trjfidsomi$n <- domo$nf + trjfidsomi$col <- domo$fcol + trjfidsomi$types <- typ ## The average pseudo-temporal expression profile of this group ## can be plotted by the function plotexpression: - par(mfrow = c(1,1)) - test$cex = 1 - second$line = 1.5 - if (trjfidsomi$name == "Title") trjfidsomi$name = "" + par(mfrow = c(1, 1)) + test$cex <- 1 + second$line <- 1.5 + if (trjfidsomi$name == "Title") trjfidsomi$name <- "" print(do.call(plotexpression, c(trjfidsomi))) - mess2 <- paste(c(trjfidsomi.use.genes), collapse=", ") + mess2 <- paste(c(trjfidsomi.use.genes), collapse = ", ") mess1 <- "Average pseudo-temporal expression profile" print(do.call(mtext, c(mess1, test))) print(do.call(mtext, c(mess2, second))) |
| b |
| diff -r 7e014059a88d -r a4b734cd253b test-data/intestinal.genelist --- a/test-data/intestinal.genelist Wed Jan 29 17:16:36 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
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| b |
| diff -r 7e014059a88d -r a4b734cd253b test-data/intestinal.pdf |
| b |
| Binary file test-data/intestinal.pdf has changed |
| b |
| diff -r 7e014059a88d -r a4b734cd253b test-data/intestinal_advanced.filter.pdf |
| b |
| Binary file test-data/intestinal_advanced.filter.pdf has changed |
| b |
| diff -r 7e014059a88d -r a4b734cd253b test-data/intestinal_advanced.genelist --- a/test-data/intestinal_advanced.genelist Wed Jan 29 17:16:36 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,251 +0,0 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| diff -r 7e014059a88d -r a4b734cd253b test-data/matrix2.genelist --- a/test-data/matrix2.genelist Wed Jan 29 17:16:36 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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