Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms

comparison readmap.xml @ 13:355940295e76 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 15:04:45 -0500
parents 2fc0d4756048
children f3e338e433ef
comparison
equal deleted inserted replaced
12:2fc0d4756048 13:355940295e76
199 pdf(file="${combi_PDF}", paper="special", height=page_height_combi, width=page_width) 199 pdf(file="${combi_PDF}", paper="special", height=page_height_combi, width=page_width)
200 for (i in seq(1,n_genes,rows_per_page/2)) { 200 for (i in seq(1,n_genes,rows_per_page/2)) {
201 start=i 201 start=i
202 end=i+rows_per_page/2-1 202 end=i+rows_per_page/2-1
203 if (end>n_genes) {end=n_genes} 203 if (end>n_genes) {end=n_genes}
204 if ("${yrange}" != 0) {readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else { 204 if (${yrange} != 0) {readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else {
205 readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-"{$yrange}", "{$yrange}"), par.settings=par.settings.readmap)) } 205 readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-${yrange}, ${yrange}), par.settings=par.settings.readmap)) }
206 size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, strip=FALSE, par.settings=par.settings.combination.size)) 206 size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, strip=FALSE, par.settings=par.settings.combination.size))
207 plot.list=rbind(read_plot.list, size_plot.list ) 207 plot.list=rbind(read_plot.list, size_plot.list )
208 args.list=c(plot.list, list(nrow=rows_per_page + extrarow, ncol=1, 208 args.list=c(plot.list, list(nrow=rows_per_page + extrarow, ncol=1,
209 main=textGrob("${title}", gp=gpar(cex=1), just="top"), 209 main=textGrob("${title}", gp=gpar(cex=1), just="top"),
210 left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90), 210 left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90),