| Previous changeset 2:87de515af823 (2019-02-28) Next changeset 4:3e5bb16abb55 (2019-08-12) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit d94b3b8a4c7cf8c604279eb1eea24d32b3868922 |
|
modified:
macros_cluster.xml scripts/cluster.R |
|
added:
test-data/intestinal.filter.log test-data/matrix.filter.geqone.pdf |
| b |
| diff -r 87de515af823 -r da7ff78fe296 macros_cluster.xml --- a/macros_cluster.xml Thu Feb 28 17:39:28 2019 -0500 +++ b/macros_cluster.xml Mon Apr 15 17:54:08 2019 -0400 |
| b |
| @@ -287,6 +287,7 @@ filt.use.ccorrect = FALSE filt.lbatch.regexes = NULL +filt.geqone = as.logical( '$filt.hist_geq_one' ) filt\$mintotal = as.integer( '$filt.mintotal' ) filt\$minexpr = as.integer( '$filt.minexpr' ) filt\$minnumber = as.integer( '$filt.minnumber' ) |
| b |
| diff -r 87de515af823 -r da7ff78fe296 scripts/cluster.R --- a/scripts/cluster.R Thu Feb 28 17:39:28 2019 -0500 +++ b/scripts/cluster.R Mon Apr 15 17:54:08 2019 -0400 |
| b |
| @@ -1,5 +1,5 @@ #!/usr/bin/env R -VERSION = "0.3" +VERSION = "0.4" args = commandArgs(trailingOnly = T) @@ -28,6 +28,10 @@ filt.lib <- log10(colSums(getfdata(sc))) filt.feat <- log10(colSums(getfdata(sc)>0)) + if (filt.geqone){ + filt.feat <- log10(colSums(getfdata(sc)>=1)) + } + br <- 50 ## Determine limits on plots based on the unfiltered data ## (doesn't work, R rejects limits and norm data is too different to compare to exp data @@ -124,11 +128,12 @@ goi <- head(rownames(dg.goi.table), genelist.plotlim) print(plotmarkergenes(sc, goi)) - print(do.call(mtext, c(paste(" Cluster ",n), test))) ## spacing is a hack + buffer <- paste(rep("", 36), collapse=" ") + print(do.call(mtext, c(paste(buffer, "Cluster ",n), test))) ## spacing is a hack test$line=-1 - print(do.call(mtext, c(paste(" Sig. Genes"), test))) ## spacing is a hack + print(do.call(mtext, c(paste(buffer, "Sig. Genes"), test))) ## spacing is a hack test$line=-2 - print(do.call(mtext, c(paste(" (fc > ", genelist.foldchange,")"), test))) ## spacing is a hack + print(do.call(mtext, c(paste(buffer, "(fc > ", genelist.foldchange,")"), test))) ## spacing is a hack }) write.table(df, file=out.genelist, sep="\t", quote=F) @@ -139,10 +144,10 @@ if (use.filtnormconf){ sc <- do.filter(sc) message(paste(" - Source:: genes:",nrow(sc@expdata),", cells:",ncol(sc@expdata))) - message(paste(" - Filter:: genes:",nrow(sc@ndata),", cells:",ncol(sc@ndata))) + message(paste(" - Filter:: genes:",nrow(getfdata(sc)),", cells:",ncol(getfdata(sc)))) message(paste(" :: ", - sprintf("%.1f", 100 * nrow(sc@ndata)/nrow(sc@expdata)), "% of genes remain,", - sprintf("%.1f", 100 * ncol(sc@ndata)/ncol(sc@expdata)), "% of cells remain")) + sprintf("%.1f", 100 * nrow(getfdata(sc))/nrow(sc@expdata)), "% of genes remain,", + sprintf("%.1f", 100 * ncol(getfdata(sc))/ncol(sc@expdata)), "% of cells remain")) } if (use.cluster){ |
| b |
| diff -r 87de515af823 -r da7ff78fe296 test-data/intestinal.filter.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/intestinal.filter.log Mon Apr 15 17:54:08 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Loading test data from library + - Source:: genes: 20268 , cells: 431 + - Filter:: genes: 2089 , cells: 287 + :: 10.3 % of genes remain, 66.6 % of cells remain |
| b |
| diff -r 87de515af823 -r da7ff78fe296 test-data/matrix.filter.geqone.pdf |
| b |
| Binary file test-data/matrix.filter.geqone.pdf has changed |