Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms
comparison plot_size_readmap.r @ 20:45df4c72a780 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 521b1e3fcf3dbf9d61d6b2b90d2415c3dadc4b5a
| author | drosofff |
|---|---|
| date | Wed, 26 Sep 2018 11:06:34 -0400 |
| parents | be0c6b6466cc |
| children |
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| 19:675033bcb79e | 20:45df4c72a780 |
|---|---|
| 97 for (i in seq(1,n_genes,rows_per_page)) { | 97 for (i in seq(1,n_genes,rows_per_page)) { |
| 98 start=i | 98 start=i |
| 99 end=i+rows_per_page-1 | 99 end=i+rows_per_page-1 |
| 100 if (end>n_genes) {end=n_genes} | 100 if (end>n_genes) {end=n_genes} |
| 101 if (args$yrange == 0) { readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else { | 101 if (args$yrange == 0) { readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else { |
| 102 readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-args.yrange, args.yrange) , par.settings=par.settings.readmap)) } | 102 readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-args$yrange, args$yrange) , par.settings=par.settings.readmap)) } |
| 103 args_list=c(readmap_plot.list, list(nrow=rows_per_page, ncol=1, | 103 args_list=c(readmap_plot.list, list(nrow=rows_per_page, ncol=1, |
| 104 top=textGrob("Read Maps (nucleotide coordinates)", gp=gpar(cex=1), just="top"), | 104 top=textGrob("Read Maps (nucleotide coordinates)", gp=gpar(cex=1), just="top"), |
| 105 left=textGrob(args$ylabel, gp=gpar(cex=1), vjust=1, rot=90) | 105 left=textGrob(args$ylabel, gp=gpar(cex=1), vjust=1, rot=90) |
| 106 ) | 106 ) |
| 107 ) | 107 ) |
| 129 for (i in seq(1,n_genes,rows_per_page/2)) { | 129 for (i in seq(1,n_genes,rows_per_page/2)) { |
| 130 start=i | 130 start=i |
| 131 end=i+rows_per_page/2-1 | 131 end=i+rows_per_page/2-1 |
| 132 if (end>n_genes) {end=n_genes} | 132 if (end>n_genes) {end=n_genes} |
| 133 if (args$yrange == 0) {readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else { | 133 if (args$yrange == 0) {readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else { |
| 134 readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-args.yrange, args.yrange), par.settings=par.settings.readmap)) } | 134 readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-args$yrange, args$yrange), par.settings=par.settings.readmap)) } |
| 135 size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, strip=FALSE, par.settings=par.settings.combination.size)) | 135 size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, strip=FALSE, par.settings=par.settings.combination.size)) |
| 136 plot.list=rbind(readmap_plot.list, size_plot.list ) | 136 plot.list=rbind(readmap_plot.list, size_plot.list ) |
| 137 args_list=c(plot.list, list(nrow=rows_per_page+1, ncol=1, | 137 args_list=c(plot.list, list(nrow=rows_per_page+1, ncol=1, |
| 138 top=textGrob(args$title, gp=gpar(cex=1), just="top"), | 138 top=textGrob(args$title, gp=gpar(cex=1), just="top"), |
| 139 left=textGrob(args$ylabel, gp=gpar(cex=1), vjust=1, rot=90), | 139 left=textGrob(args$ylabel, gp=gpar(cex=1), vjust=1, rot=90), |