Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms

comparison readmap.xml @ 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
comparison
equal deleted inserted replaced
14:f3e338e433ef 15:16d0811f7a09
166 pdf(file="${readmap_PDF}", paper="special", height=page_height_simple, width=page_width) 166 pdf(file="${readmap_PDF}", paper="special", height=page_height_simple, width=page_width)
167 for (i in seq(1,n_genes,rows_per_page)) { 167 for (i in seq(1,n_genes,rows_per_page)) {
168 start=i 168 start=i
169 end=i+rows_per_page-1 169 end=i+rows_per_page-1
170 if (end>n_genes) {end=n_genes} 170 if (end>n_genes) {end=n_genes}
171 readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) 171 if (${yrange} == 0) { readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else {
172 readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-${yrange}, ${yrange}) , par.settings=par.settings.readmap)) }
172 args.list=c(readmap_plot.list, list(nrow=rows_per_page, ncol=1, 173 args.list=c(readmap_plot.list, list(nrow=rows_per_page, ncol=1,
173 main=textGrob("Read Maps (nucleotide coordinates)", gp=gpar(cex=1), just="top"), 174 main=textGrob("Read Maps (nucleotide coordinates)", gp=gpar(cex=1), just="top"),
174 left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90) 175 left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90)
175 #sub=textGrob("readmap coordinates", gp=gpar(cex=.75), just="bottom") 176 #sub=textGrob("readmap coordinates", gp=gpar(cex=.75), just="bottom")
176 ) 177 )
199 pdf(file="${combi_PDF}", paper="special", height=page_height_combi, width=page_width) 200 pdf(file="${combi_PDF}", paper="special", height=page_height_combi, width=page_width)
200 for (i in seq(1,n_genes,rows_per_page/2)) { 201 for (i in seq(1,n_genes,rows_per_page/2)) {
201 start=i 202 start=i
202 end=i+rows_per_page/2-1 203 end=i+rows_per_page/2-1
203 if (end>n_genes) {end=n_genes} 204 if (end>n_genes) {end=n_genes}
204 if (${yrange} != 0) {readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else { 205 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}, ${yrange}), par.settings=par.settings.readmap)) } 206 readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-${yrange}, ${yrange}), par.settings=par.settings.readmap)) }
206 size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, strip=FALSE, par.settings=par.settings.combination.size)) 207 size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, strip=FALSE, par.settings=par.settings.combination.size))
207 plot.list=rbind(readmap_plot.list, size_plot.list ) 208 plot.list=rbind(readmap_plot.list, size_plot.list )
208 args.list=c(plot.list, list(nrow=rows_per_page + extrarow, ncol=1, 209 args.list=c(plot.list, list(nrow=rows_per_page + extrarow, ncol=1,
209 main=textGrob("${title}", gp=gpar(cex=1), just="top"), 210 main=textGrob("${title}", gp=gpar(cex=1), just="top"),