# Phloseq Ordination Plot

A Galaxy tool to produce NMDS plots using Phyloseq from either a BIOM1 file or 2 input tables.

Currently produces the plots embedded in a html file for output with links to a PDF file.

Requires:

Phyloseq 1.22.3
r-getopt 1.20.0
r-doparallel 1.0.11
ghostscript 9.18


### Run phyloseq_ordination_plot.R with three input files
Rscript 'phyloseq_ordination_plot.R' --otu_table='GP_OTU_TABLE.txt' --tax_table='GP_TAX_TABLE.txt' --meta_table='GP_SAMPLE_TABLE.txt' --method='bray' --kingdom=2 --cutoff=5 --category=6 --outdir='outputdir' --htmlfile='test.html'

### Run phyloseq_nmds.R with biom file
Rscript 'phyloseq_ordinate_plot.R' --biom='GP.biom' --subset='Primer' --method='NMDS' --distance='bray' --kingdom='Phylum' --plottype='2' --outdir='outputdir' --htmlfile='biom_out.html'

## Version history:

**XML Wrapper:**

Alpha version by Michael Thang of QFAB, Australia.

1.22.3.1: Simon Gladman Melbourne Bioinformatics

* Incorporated tests
* Requirements
* Version statement
* Citations

1.22.3.2: Michael Thang QFAB, Simon Gladman Melbourne Bioinformatics

* Uses new version of BIOM1 datatype to get metadata
* Output label changed as per user requirements


**R Script: phyloseq_nmds.R**

0.1.0: Michael Thang QFAB

* Original version

0.1.1: Michael Thang QFAB

* Added extra BIOM import functionality so it doesn't solely rely on phyloseq's internal importer.

0.1.2: Michael Thang QFAB

* BIOM functionality now requires the column header name in text.