Mercurial > repos > qfabrepo > metadegalaxy_phyloseq_richness

comparison phyloseq_richness.r @ 0:0ab4501d805b draft

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"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
author qfabrepo
date Mon, 14 Sep 2020 07:38:57 +0000
parents
children e0225f3e8ef6
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-1:000000000000 0:0ab4501d805b
1 library('getopt')
2 suppressPackageStartupMessages(library('phyloseq'))
3 Sys.setenv("DISPLAY"=":1")
4
5 options(warn=-1)
6 option_specification = matrix(c(
7 'biomfile','b',2,'character',
8 'metafile','m',2,'character',
9 'xcolumn','x',2,'numeric',
10 'lcolumn','l',2,'numeric',
11 'outdir','o',2,'character',
12 'htmlfile','h',2,'character'
13 ),byrow=TRUE,ncol=4);
14
15
16 options <- getopt(option_specification);
17 options(bitmapType="cairo")
18
19
20 if (!is.null(options$outdir)) {
21 # Create the directory
22 dir.create(options$outdir,FALSE)
23 }
24
25
26 galaxy_biom <- import_biom(options$biomfile)
27 galaxy_map <- import_qiime_sample_data(options$metafile)
28 tax_col_norm <- c("Kingdom","Phylum","Class","Order","Family","Genus","Species")
29 tax_col_extra <- c("None","Kingdom","Phylum","Class","Order","Family","Genus","Species")
30
31 number.of.tax.rank<-length(colnames(tax_table(galaxy_biom)))
32
33 if( number.of.tax.rank == 7){
34 colnames(tax_table(galaxy_biom)) <- tax_col_norm
35 }else{
36 colnames(tax_table(galaxy_biom)) <- tax_col_extra
37 }
38
39
40 AIP_galaxy <- merge_phyloseq(galaxy_biom,galaxy_map)
41
42
43 x.selectedColumn<-colnames(galaxy_map)[options$xcolumn]
44 l.selectedColumn<-colnames(galaxy_map)[options$lcolumn]
45
46
47
48
49 pdffile <- gsub("[ ]+", "", paste(options$outdir,"/pdffile.pdf"))
50 pngfile_richness <- gsub("[ ]+", "", paste(options$outdir,"/richness.png"))
51 htmlfile <- gsub("[ ]+", "", paste(options$htmlfile))
52
53
54 # Produce PDF file
55 pdf(pdffile);
56 plot_richness(AIP_galaxy,measures=c("Observed"),color=l.selectedColumn,x=x.selectedColumn)
57 garbage<-dev.off();
58
59 #png('richness.png')
60 bitmap(pngfile_richness,"png16m")
61 plot_richness(AIP_galaxy,measures=c("Observed"),color=l.selectedColumn,x=x.selectedColumn)
62 garbage<-dev.off()
63
64 # Produce the HTML file
65 htmlfile_handle <- file(htmlfile)
66 html_output = c('<html><body>',
67 '<table align="center">',
68 '<tr>',
69 '<td valign="middle" style="vertical-align:middle;">',
70 '<a href="pdffile.pdf"><img src="richness.png"/></a>',
71 '</td>',
72 '</tr>',
73 '</table>',
74 '<table align="center>',
75 '<tr>',
76 '<td valign="middle" style="vertical-align:middle;">',
77 '<a href="pdffile.pdf"><img src="richness.png"/></a>',
78 '</td>',
79 '</tr>',
80 '</table>',
81 '</html></body>');
82 writeLines(html_output, htmlfile_handle);
83 close(htmlfile_handle);