Mercurial > repos > simon-gladman > phyloseq_ordination_plot

comparison README.md @ 1:52f009b255a1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Updated tool
author simon-gladman
date Thu, 22 Nov 2018 07:07:27 -0500
parents
children
comparison
equal deleted inserted replaced
0:ae9cd53b7760 1:52f009b255a1
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.