Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms
comparison readmap.xml @ 21:6fbd21abde56 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 78fca5d46c4554514bc51b0010a7611aaced40b9-dirty
| author | drosofff |
|---|---|
| date | Thu, 04 Feb 2016 08:28:38 -0500 |
| parents | 99f478136171 |
| children | dbac07fc9186 |
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| 20:99f478136171 | 21:6fbd21abde56 |
|---|---|
| 156 ## end of function parameters' | 156 ## end of function parameters' |
| 157 | 157 |
| 158 ## GRAPHS | 158 ## GRAPHS |
| 159 | 159 |
| 160 if (n_genes > 7) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=${rows_per_page}; extrarow=0 } else { | 160 if (n_genes > 7) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=${rows_per_page}; extrarow=0 } else { |
| 161 rows_per_page= n_genes; page_height_simple = 1.67*n_genes; page_height_combi=page_height_simple*2; extrarow=0 } | 161 rows_per_page= n_genes; page_height_simple = 2.5*n_genes; page_height_combi=page_height_simple*2; extrarow=0 } |
| 162 ## rows_per_page= 8; page_height_simple = 11.69/7*n_genes; page_height_combi=11.69/9*(n_genes*2); extrarow=0 } | 162 ## rows_per_page= 8; page_height_simple = 11.69/7*n_genes; page_height_combi=11.69/9*(n_genes*2); extrarow=0 } |
| 163 ## rows_per_page= n_genes; page_height_simple = 11.69/n_genes/4; page_height_combi=11.69/(n_genes*2); extrarow=1 } | 163 ## rows_per_page= n_genes; page_height_simple = 11.69/n_genes/4; page_height_combi=11.69/(n_genes*2); extrarow=1 } |
| 164 if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 8.2677*n_samples/3} # to test | 164 if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 8.2677*n_samples/3} # to test |
| 165 | 165 |
| 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) |
| 196 do.call(grid.arrange, args.list) | 196 do.call(grid.arrange, args.list) |
| 197 } | 197 } |
| 198 devname=dev.off() | 198 devname=dev.off() |
| 199 | 199 |
| 200 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) |
| 201 if (rows_per_page %% 2 != 0) { rows_per_page = rows_per_page + 1} | |
| 201 for (i in seq(1,n_genes,rows_per_page/2)) { | 202 for (i in seq(1,n_genes,rows_per_page/2)) { |
| 202 start=i | 203 start=i |
| 203 end=i+rows_per_page/2-1 | 204 end=i+rows_per_page/2-1 |
| 204 if (end>n_genes) {end=n_genes} | 205 if (end>n_genes) {end=n_genes} |
| 205 if (${yrange} == 0) {readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else { | 206 if (${yrange} == 0) {readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else { |