|
1
|
1 # Phloseq Ordination Plot
|
|
|
2
|
|
|
3 A Galaxy tool to produce NMDS plots using Phyloseq from either a BIOM1 file or 2 input tables.
|
|
|
4
|
|
|
5 Currently produces the plots embedded in a html file for output with links to a PDF file.
|
|
|
6
|
|
|
7 Requires:
|
|
|
8
|
|
|
9 Phyloseq 1.22.3
|
|
|
10 r-getopt 1.20.0
|
|
|
11 r-doparallel 1.0.11
|
|
|
12 ghostscript 9.18
|
|
|
13
|
|
|
14
|
|
|
15 ### Run phyloseq_ordination_plot.R with three input files
|
|
|
16 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'
|
|
|
17
|
|
|
18 ### Run phyloseq_nmds.R with biom file
|
|
|
19 Rscript 'phyloseq_ordinate_plot.R' --biom='GP.biom' --subset='Primer' --method='NMDS' --distance='bray' --kingdom='Phylum' --plottype='2' --outdir='outputdir' --htmlfile='biom_out.html'
|
|
|
20
|
|
|
21 ## Version history:
|
|
|
22
|
|
|
23 **XML Wrapper:**
|
|
|
24
|
|
|
25 Alpha version by Michael Thang of QFAB, Australia.
|
|
|
26
|
|
|
27 1.22.3.1: Simon Gladman Melbourne Bioinformatics
|
|
|
28
|
|
|
29 * Incorporated tests
|
|
|
30 * Requirements
|
|
|
31 * Version statement
|
|
|
32 * Citations
|
|
|
33
|
|
|
34 1.22.3.2: Michael Thang QFAB, Simon Gladman Melbourne Bioinformatics
|
|
|
35
|
|
|
36 * Uses new version of BIOM1 datatype to get metadata
|
|
|
37 * Output label changed as per user requirements
|
|
|
38
|
|
|
39
|
|
|
40 **R Script: phyloseq_nmds.R**
|
|
|
41
|
|
|
42 0.1.0: Michael Thang QFAB
|
|
|
43
|
|
|
44 * Original version
|
|
|
45
|
|
|
46 0.1.1: Michael Thang QFAB
|
|
|
47
|
|
|
48 * Added extra BIOM import functionality so it doesn't solely rely on phyloseq's internal importer.
|
|
|
49
|
|
|
50 0.1.2: Michael Thang QFAB
|
|
|
51
|
|
|
52 * BIOM functionality now requires the column header name in text.
|
