Mercurial > repos > qfabrepo > metadegalaxy_phyloseq_richness
view phyloseq_richness.r @ 0:0ab4501d805b draft
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
author | qfabrepo |
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date | Mon, 14 Sep 2020 07:38:57 +0000 |
parents | |
children | e0225f3e8ef6 |
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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', '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] pdffile <- gsub("[ ]+", "", paste(options$outdir,"/pdffile.pdf")) pngfile_richness <- gsub("[ ]+", "", paste(options$outdir,"/richness.png")) htmlfile <- gsub("[ ]+", "", paste(options$htmlfile)) # Produce PDF file pdf(pdffile); plot_richness(AIP_galaxy,measures=c("Observed"),color=l.selectedColumn,x=x.selectedColumn) garbage<-dev.off(); #png('richness.png') bitmap(pngfile_richness,"png16m") plot_richness(AIP_galaxy,measures=c("Observed"),color=l.selectedColumn,x=x.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="pdffile.pdf"><img src="richness.png"/></a>', '</td>', '</tr>', '</table>', '<table align="center>', '<tr>', '<td valign="middle" style="vertical-align:middle;">', '<a href="pdffile.pdf"><img src="richness.png"/></a>', '</td>', '</tr>', '</table>', '</html></body>'); writeLines(html_output, htmlfile_handle); close(htmlfile_handle);