Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms

changeset 15:16d0811f7a09 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit e27d18d58ae095e7fad4b08b04370857a1d37964-dirty
author mvdbeek
date Tue, 02 Feb 2016 15:28:12 -0500
parents f3e338e433ef
children 70f4385534f9
files readmap.xml
diffstat 1 files changed, 3 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/readmap.xml	Tue Feb 02 15:15:43 2016 -0500
+++ b/readmap.xml	Tue Feb 02 15:28:12 2016 -0500
@@ -168,7 +168,8 @@
         start=i
         end=i+rows_per_page-1
         if (end>n_genes) {end=n_genes}
-        readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap))
+        if (${yrange} == 0) { readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else {
+        readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-${yrange}, ${yrange}) , par.settings=par.settings.readmap)) }
         args.list=c(readmap_plot.list, list(nrow=rows_per_page, ncol=1,
                                             main=textGrob("Read Maps (nucleotide coordinates)", gp=gpar(cex=1), just="top"),
                                             left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90)
@@ -201,7 +202,7 @@
         start=i
         end=i+rows_per_page/2-1
         if (end>n_genes) {end=n_genes}
-        if (${yrange} != 0) {readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else {
+        if (${yrange} == 0) {readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else {
         readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-${yrange}, ${yrange}), par.settings=par.settings.readmap)) }
         size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, strip=FALSE, par.settings=par.settings.combination.size))
 	plot.list=rbind(readmap_plot.list, size_plot.list )