Mercurial > repos > qfabrepo > metadegalaxy_phyloseq_abundance_taxonomy

diff phyloseq_abundance_taxonomy.r @ 0:b2fafdd3533d draft default tip

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"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
author qfabrepo
date Mon, 14 Sep 2020 08:07:43 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_abundance_taxonomy.r	Mon Sep 14 08:07:43 2020 +0000
@@ -0,0 +1,76 @@
+library('getopt')
+suppressPackageStartupMessages(library('phyloseq'))
+Sys.setenv("DISPLAY"=":1")
+
+options(warn=-1)
+option_specification = matrix(c(
+   'biomfile','b',2,'character',
+   'metafile','m',2,'character',
+     'xcolumn','x',2,'numeric',
+     'lcolumn','l',2,'numeric',
+     'taxonomy','t',2,'character',
+     'outdir','o',2,'character',
+   'htmlfile','h',2,'character'
+),byrow=TRUE,ncol=4);
+
+
+options <- getopt(option_specification);
+options(bitmapType="cairo")
+ 
+
+if (!is.null(options$outdir)) {
+  # Create the directory
+  dir.create(options$outdir,FALSE)
+}
+
+
+galaxy_biom <- import_biom(options$biomfile)
+galaxy_map <- import_qiime_sample_data(options$metafile)
+tax_col_norm <- c("Kingdom","Phylum","Class","Order","Family","Genus","Species")
+tax_col_extra <- c("None","Kingdom","Phylum","Class","Order","Family","Genus","Species")
+
+number.of.tax.rank<-length(colnames(tax_table(galaxy_biom)))
+
+if( number.of.tax.rank == 7){
+colnames(tax_table(galaxy_biom)) <- tax_col_norm
+}else{
+colnames(tax_table(galaxy_biom)) <- tax_col_extra
+}
+
+
+AIP_galaxy <- merge_phyloseq(galaxy_biom,galaxy_map)
+
+
+x.selectedColumn<-colnames(galaxy_map)[options$xcolumn]
+l.selectedColumn<-colnames(galaxy_map)[options$lcolumn]
+
+tax.selected<-options$taxonomy
+
+pdffile <- gsub("[ ]+", "", paste(options$outdir,"/kingdom.pdf"))
+pngfile_kingdom <- gsub("[ ]+", "", paste(options$outdir,"/kingdom.png"))
+htmlfile <- gsub("[ ]+", "", paste(options$htmlfile))
+
+
+# Produce PDF file
+pdf(pdffile);
+plot_bar(AIP_galaxy,x=x.selectedColumn,facet_grid = paste('~', tax.selected),fill=l.selectedColumn)
+garbage<-dev.off();
+
+#png('kingdom.png')
+bitmap(pngfile_kingdom,"png16m")
+plot_bar(AIP_galaxy,x=x.selectedColumn,facet_grid = paste('~', tax.selected),fill=l.selectedColumn)
+garbage<-dev.off()
+
+# Produce the HTML file
+htmlfile_handle <- file(htmlfile)
+html_output = c('<html><body>',
+	            '<table align="center">',
+		        '<tr>',
+		        '<td valign="middle" style="vertical-align:middle;">',
+                '<a href="kingdom.pdf"><img src="kingdom.png"/></a>',
+		        '</td>',
+		        '</tr>',
+		        '</table>',
+                '</html></body>');
+writeLines(html_output, htmlfile_handle);
+close(htmlfile_handle);