# HG changeset patch
# User qfabrepo
# Date 1600070528 0
# Node ID 3856a1590a1175c542057bd7e5708c83674478ab
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
diff -r 000000000000 -r 3856a1590a11 phyloseq_abundance_factor.r
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_abundance_factor.r Mon Sep 14 08:02:08 2020 +0000
@@ -0,0 +1,91 @@
+
+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('',
+ '',
+ '',
+ '',
+ ' ',
+ ' ',
+ '
',
+ '');
+writeLines(html_output, htmlfile_handle);
+close(htmlfile_handle);
diff -r 000000000000 -r 3856a1590a11 phyloseq_abundance_factor.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_abundance_factor.xml Mon Sep 14 08:02:08 2020 +0000
@@ -0,0 +1,108 @@
+
+ Phyloseq Abundance Plot with the factors of choice
+
+ r-base
+ bioconductor-phyloseq
+ r-getopt
+ ghostscript
+
+ /dev/null | grep -v -i "WARNING: ")
+ ]]>
+
+
+
+
+
+
+ 1
+ 2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+Creates an abundance barplot using an R package called phyloseq_.
+
+.. _phyloseq: https://joey711.github.io/phyloseq/plot_bar-examples.html
+
+-----
+
+**Input**
+
+
+- **BIOM file** - this is a BIOM_ file format
+- **Metadata file** - this is a metadata file of the experiment design
+- **Column used for X-axis** - The horizontal x-axis display on the barplot.
+- **Column used as legend** - select a group from the metadata to fill color to represent the group it belongs to.
+- **Is this one factor or two factor** - This is the facet_grid feature of phyloseq's plot_bar to allow plotting with two factors (e.g, facet_grid=~protein + allergy)
+- **Column used as factor 1** - select the first factor for facet_grid feature from the metadata file
+
+.. _BIOM: http://biom-format.org/
+
+-----
+
+=========
+Resources
+=========
+
+**Wrapper Authors**
+
+QFAB Bioinformatics (support@qfab.org)
+
+
+
+ 10.18129/B9.bioc.phyloseq
+ doi:10.1186/2047-217X-1-7
+
+
diff -r 000000000000 -r 3856a1590a11 test-data/abundace_factor.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abundace_factor.html Mon Sep 14 08:02:08 2020 +0000
@@ -0,0 +1,9 @@
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 3856a1590a11 test-data/biom_out.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/biom_out.html Mon Sep 14 08:02:08 2020 +0000
@@ -0,0 +1,9 @@
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 3856a1590a11 test-data/metadata.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/metadata.txt Mon Sep 14 08:02:08 2020 +0000
@@ -0,0 +1,19 @@
+#SampleID dpw time Food Replicate_Group
+F3D0 0 Early None Group1
+F3D1 1 Early None Group1
+F3D2 2 Early None Group1
+F3D3 3 Early Cheddar Group2
+F3D5 5 Early Cheddar Group2
+F3D6 6 Early Cheddar Group2
+F3D7 7 Early Swiss Group3
+F3D8 8 Early Swiss Group3
+F3D9 9 Early Swiss Group3
+F3D141 141 Late Cheddar Group4
+F3D142 142 Late Cheddar Group4
+F3D143 143 Late Cheddar Group4
+F3D144 144 Late None Group5
+F3D145 145 Late None Group5
+F3D146 146 Late None Group5
+F3D147 147 Late Swiss Group6
+F3D148 148 Late Swiss Group6
+F3D149 149 Late Swiss Group6
diff -r 000000000000 -r 3856a1590a11 test-data/test.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.biom Mon Sep 14 08:02:08 2020 +0000
@@ -0,0 +1,1 @@
+{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2017-09-08T01:49:15.647451","type": "OTU table","matrix_element_type": "float","shape": [5339, 18],"data": 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