| Previous changeset 8:f911a64454fb (2021-12-20) Next changeset 10:49776718ae90 (2024-11-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf |
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modified:
macros.xml macros_cheetah.xml raceid_clustering.xml scripts/cluster.R scripts/clusterinspect.R scripts/trajectoryinspect.R |
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| diff -r f911a64454fb -r 0bff0ee0683a macros.xml --- a/macros.xml Mon Dec 20 10:12:47 2021 +0000 +++ b/macros.xml Wed Aug 24 18:09:06 2022 +0000 |
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| @@ -26,7 +26,7 @@ } </token> <token name="@TOOL_VERSION@">0.2.3</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> <token name="@PROFILE@">21.01</token> <macro name="version_command_config" token_prog="temp" token_cheetah="temp2" token_out="2> '$outlog'"> |
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| diff -r f911a64454fb -r 0bff0ee0683a macros_cheetah.xml --- a/macros_cheetah.xml Mon Dec 20 10:12:47 2021 +0000 +++ b/macros_cheetah.xml Wed Aug 24 18:09:06 2022 +0000 |
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| @@ -104,7 +104,6 @@ clust.clustexp\$cln = as.integer( '$clust.use.cln' ) clust.clustexp\$clustnr = as.integer( '$clust.use.clustnr' ) clust.clustexp\$bootnr = as.integer( '$clust.use.bootnr' ) -##clust.clustexp\$rseed = as.integer( '$clust.use.rseed' ) #end if #end if @@ -313,12 +312,12 @@ <token name="@INSPECTTRAJECTORIES_CHEETAH@"><![CDATA[ in.rdat = readRDS('${inputrds}') -perform.stemID = FALSE -perform.fateID = FALSE -perform.fateID.sominspect = FALSE +perform.stemid = FALSE +perform.fateid = FALSE +perform.fateid.sominspect = FALSE #if str($trjsid.basic.doit) == "yes" -perform.stemID = TRUE +perform.stemid = TRUE trjsid.getproj = formals(getproj) trjsid.numdiffgenes = 10 @@ -334,29 +333,29 @@ #end if #if str($trjfid.basic.doit) == "yes": -perform.fateID = TRUE -trjfid.cellsfrom = formals(cellsfromtree) -trjfid.filterset = formals(filterset) -trjfid.getsom = formals(getsom) -trjfid.procsom = formals(procsom) -trjfid.plotheat = list() +perform.fateid = TRUE +trjfid_cellsfrom = formals(cellsfromtree) +trjfid_filterset = formals(filterset) +trjfid_getsom = formals(getsom) +trjfid_procsom = formals(procsom) +trjfid_plotheat = list() -trjfid.cellsfrom\$z = string2numericvector( '$trjfid.basic.cellsfromz' ) +trjfid_cellsfrom\$z = string2numericvector( '$trjfid.basic.cellsfromz' ) #if str($trjfid.basic.use.def) == "no": -trjfid.filterset\$minexpr = as.integer( '$trjfid.basic.use.filterset_minexpr' ) -trjfid.filterset\$minnumber = as.integer( '$trjfid.basic.use.filterset_minnumber' ) -trjfid.getsom\$nb = as.numeric( '$trjfid.basic.use.getsom_nb' ) -trjfid.getsom\$alpha = as.numeric( '$trjfid.basic.use.getsom_alpha' ) -trjfid.procsom\$corthr = as.numeric( '$trjfid.basic.use.procsom_corthr' ) -trjfid.procsom\$minsom = as.integer( '$trjfid.basic.use.procsom_minsom' ) -trjfid.plotheat\$xgrid = as.logical( '$trjfid.basic.use.plotheat_xgrid' ) -trjfid.plotheat\$ygrid = as.logical( '$trjfid.basic.use.plotheat_ygrid' ) -trjfid.plotheat\$xlab = as.logical( '$trjfid.basic.use.plotheat_xlab' ) +trjfid_filterset\$minexpr = as.integer( '$trjfid.basic.use.filterset_minexpr' ) +trjfid_filterset\$minnumber = as.integer( '$trjfid.basic.use.filterset_minnumber' ) +trjfid_getsom\$nb = as.numeric( '$trjfid.basic.use.getsom_nb' ) +trjfid_getsom\$alpha = as.numeric( '$trjfid.basic.use.getsom_alpha' ) +trjfid_procsom\$corthr = as.numeric( '$trjfid.basic.use.procsom_corthr' ) +trjfid_procsom\$minsom = as.integer( '$trjfid.basic.use.procsom_minsom' ) +trjfid_plotheat\$xgrid = as.logical( '$trjfid.basic.use.plotheat_xgrid' ) +trjfid_plotheat\$ygrid = as.logical( '$trjfid.basic.use.plotheat_ygrid' ) +trjfid_plotheat\$xlab = as.logical( '$trjfid.basic.use.plotheat_xlab' ) #end if #if str($trjfid.basic.som.doit) == "yes": -perform.fateID.sominspect = TRUE +perform.fateid.sominspect = TRUE trjfidsomi = list() #if str($trjfid.basic.som.use_genes.typer) == "genelist": |
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| diff -r f911a64454fb -r 0bff0ee0683a raceid_clustering.xml --- a/raceid_clustering.xml Mon Dec 20 10:12:47 2021 +0000 +++ b/raceid_clustering.xml Wed Aug 24 18:09:06 2022 +0000 |
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| @@ -33,7 +33,6 @@ <param name="samp" type="integer" min="0" optional="true" label="Sample random number of cells" help="Number of random sample of cells used for the inference of cluster number and Jaccard similarity" /><!-- 0:NULL --> <param name="cln" type="integer" min="0" optional="true" label="Number of clusters" /><!-- 0:Null --> <param name="bootnr" type="integer" min="0" value="50" label="Number of booststrapping runs" /> - <param name="rseed" type="integer" value="17000" label="Random seed" /> </expand> </section> <section name="outlier" title="Outliers" expanded="true" > |
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| diff -r f911a64454fb -r 0bff0ee0683a scripts/cluster.R --- a/scripts/cluster.R Mon Dec 20 10:12:47 2021 +0000 +++ b/scripts/cluster.R Wed Aug 24 18:09:06 2022 +0000 |
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| @@ -1,7 +1,7 @@ #!/usr/bin/env R VERSION <- "0.5" # nolint -args <- commandArgs(trailingOnly = T) +args <- commandArgs(trailingOnly = TRUE) if (length(args) != 1) { message(paste("VERSION:", VERSION)) @@ -52,8 +52,8 @@ if (filt.use.ccorrect) { par(mfrow = c(2, 2)) sc <- do.call(CCcorrect, c(sc, filt.ccc)) - print(plotdimsat(sc, change = T)) - print(plotdimsat(sc, change = F)) + print(plotdimsat(sc, change = TRUE)) + print(plotdimsat(sc, change = FALSE)) } return(sc) } @@ -62,8 +62,8 @@ sc <- do.call(compdist, c(sc, clust.compdist)) sc <- do.call(clustexp, c(sc, clust.clustexp)) if (clust.clustexp$sat) { - print(plotsaturation(sc, disp = F)) - print(plotsaturation(sc, disp = T)) + print(plotsaturation(sc, disp = FALSE)) + print(plotsaturation(sc, disp = TRUE)) } print(plotjaccard(sc)) return(sc) @@ -125,7 +125,7 @@ print(do.call(mtext, c(paste(buffer, "(fc > ", genelist.foldchange, ")"), test))) }) - write.table(df, file = out.genelist, sep = "\t", quote = F) + write.table(df, file = out.genelist, sep = "\t", quote = FALSE) } @@ -138,7 +138,7 @@ is.outlier = names(dat) %in% sc@out$out) write.table(tab, file = out.assignments, sep = "\t", - quote = F, row.names = F) + quote = FALSE, row.names = FALSE) } @@ -158,7 +158,7 @@ getfdata(sc))) / ncol(sc@expdata)), "% of cells remain")) write.table(as.matrix(sc@ndata), file = out.table, col.names = NA, - row.names = T, sep = "\t", quote = F) + row.names = TRUE, sep = "\t", quote = FALSE) } if (use.cluster) { |
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| diff -r f911a64454fb -r 0bff0ee0683a scripts/clusterinspect.R --- a/scripts/clusterinspect.R Mon Dec 20 10:12:47 2021 +0000 +++ b/scripts/clusterinspect.R Wed Aug 24 18:09:06 2022 +0000 |
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| @@ -1,7 +1,7 @@ #!/usr/bin/env R VERSION <- "0.5" # nolint -args <- commandArgs(trailingOnly = T) +args <- commandArgs(trailingOnly = TRUE) if (length(args) != 1) { message(paste("VERSION:", VERSION)) @@ -74,12 +74,10 @@ use_names <- NULL if (!is.null(lob$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)] - } - else if (!is.null(lob$cln)) { + }else if (!is.null(lob$cln)) { use_names <- names(sc@cpart)[sc@cpart %in% lob$cln] } if (is.null(use_names)) { @@ -112,19 +110,23 @@ title <- paste(":", plotexp$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$fr <- TRUE print(do.call(plotexpmap, c(sc, plotexp))) print(do.call(mtext, c(paste("FR (Log)", title), test))) |
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| diff -r f911a64454fb -r 0bff0ee0683a scripts/trajectoryinspect.R --- a/scripts/trajectoryinspect.R Mon Dec 20 10:12:47 2021 +0000 +++ b/scripts/trajectoryinspect.R Wed Aug 24 18:09:06 2022 +0000 |
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| @@ -1,7 +1,7 @@ #!/usr/bin/env R VERSION <- "0.2" # nolint -args <- commandArgs(trailingOnly = T) +args <- commandArgs(trailingOnly = TRUE) if (length(args) != 1) { message(paste("VERSION:", VERSION)) @@ -19,7 +19,7 @@ second$cex <- 0.5 second$line <- 2.5 -do.trajectoryinspection.stemID <- function(ltr) { # nolint +do.trajectoryinspection.stemid <- function(ltr) { # nolint makeBranchLink <- function(i, j, k) { # nolint ingoing <- paste(sort(c(i, j)), collapse = ".") outgoing <- paste(sort(c(j, k)), collapse = ".") @@ -51,57 +51,57 @@ print(do.call(mtext, c("Final Clusters (F-R)", test))) } -do.trajectoryinspection.fateID <- function(ltr) { # nolint - n <- do.call(cellsfromtree, c(ltr, trjfid.cellsfrom)) +do.trajectoryinspection.fateid <- function(ltr) { # nolint + n <- do.call(cellsfromtree, c(ltr, trjfid_cellsfrom)) x <- getfdata(ltr@sc) - trjfid.filterset$x <- x - trjfid.filterset$n <- n$f - fs <- do.call(filterset, c(trjfid.filterset)) - trjfid.getsom$x <- fs - s1d <- do.call(getsom, c(trjfid.getsom)) - trjfid.procsom$s1d <- s1d - ps <- do.call(procsom, c(trjfid.procsom)) + trjfid_filterset$x <- x + trjfid_filterset$n <- n$f + fs <- do.call(filterset, c(trjfid_filterset)) + trjfid_getsom$x <- fs + s1d <- do.call(getsom, c(trjfid_getsom)) + 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) - print(do.call(plotheatmap, c(trjfid.plotheat))) + 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))) ##Plot z-score profile of each gene ordered by SOM modules: - trjfid.plotheat$x <- ps$all.z - trjfid.plotheat$ypart <- ps$nodes - print(do.call(plotheatmap, c(trjfid.plotheat))) + trjfid_plotheat$x <- ps$all.z + trjfid_plotheat$ypart <- ps$nodes + print(do.call(plotheatmap, c(trjfid_plotheat))) 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 - print(do.call(plotheatmap, c(trjfid.plotheat))) + trjfid_plotheat$x <- ps$all.e + trjfid_plotheat$ypart <- ps$nodes + print(do.call(plotheatmap, c(trjfid_plotheat))) 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))) + 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$f)) } -do.trajectoryinspection.fateID.sominspect <- function(domo) { # nolint +do.trajectoryinspection.fateid.sominspect <- function(domo) { # nolint g <- trjfidsomi.use.genes if (class(g) == "numeric") { g <- names(ps$nodes)[ps$nodes %in% g] @@ -135,11 +135,11 @@ ltr <- in.rdat pdf(out.pdf) -if (perform.stemID) do.trajectoryinspection.stemID(ltr) -if (perform.fateID) { - domo <- do.trajectoryinspection.fateID(ltr) - if (perform.fateID.sominspect) { - do.trajectoryinspection.fateID.sominspect(domo) +if (perform.stemid) do.trajectoryinspection.stemid(ltr) +if (perform.fateid) { + domo <- do.trajectoryinspection.fateid(ltr) + if (perform.fateid.sominspect) { + do.trajectoryinspection.fateid.sominspect(domo) } } dev.off() |