Mercurial > repos > qfabrepo > metadegalaxy_phyloseq_abundance_factor


library('getopt')
suppressPackageStartupMessages(library('phyloseq'))
Sys.setenv("DISPLAY"=":1")


cmd_args <- commandArgs(TRUE)
options(warn=-1)
option_specification = matrix(c(
   'biomfile','b',2,'character',
   'metafile','m',2,'character',
     'xcolumn','x',2,'numeric',
     'lcolumn','l',2,'numeric',
     'factor1','f1',2,'numeric',
     'factor2','f2',1,'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)


pdffile <- gsub("[ ]+", "", paste(options$outdir,"/abundance.pdf"))
pngfile_abundance <- gsub("[ ]+", "", paste(options$outdir,"/abundance.png"))
htmlfile <- gsub("[ ]+", "", paste(options$htmlfile))


###### To obtain the column name in metadata ################
x.selectedColumn<-colnames(galaxy_map)[options$xcolumn]
l.selectedColumn<-colnames(galaxy_map)[options$lcolumn]
f1.selectedColumn<-colnames(galaxy_map)[options$factor1]

factor.var <- f1.selectedColumn

if(!is.null(options$factor2)){
f2.selectedColumn<-colnames(galaxy_map)[options$factor2]
factor.var <- paste(f1.selectedColumn,f2.selectedColumn,sep="+")
}


# Produce PDF file
pdf(pdffile);
plot_bar(AIP_galaxy,x=x.selectedColumn,facet_grid = paste('~', factor.var),fill=l.selectedColumn)
garbage<-dev.off();

#png('abundance_1.png')
bitmap(pngfile_abundance,"png16m")
plot_bar(AIP_galaxy,x=x.selectedColumn,facet_grid = paste('~', factor.var),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="abundance.pdf"><img src="abundance.png"/></a>',
		        '</td>',
		        '</tr>',
		        '</table>',
                '</html></body>');
writeLines(html_output, htmlfile_handle);
close(htmlfile_handle);
author	qfabrepo
date	Mon, 14 Sep 2020 08:02:08 +0000
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