Mercurial > repos > qfabrepo > metadegalaxy_phyloseq_abundance_factor

comparison phyloseq_abundance_factor.r @ 0:3856a1590a11 draft default tip

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"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
author qfabrepo
date Mon, 14 Sep 2020 08:02:08 +0000
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-1:000000000000 0:3856a1590a11
1
2 library('getopt')
3 suppressPackageStartupMessages(library('phyloseq'))
4 Sys.setenv("DISPLAY"=":1")
5
6
7 cmd_args <- commandArgs(TRUE)
8 options(warn=-1)
9 option_specification = matrix(c(
10 'biomfile','b',2,'character',
11 'metafile','m',2,'character',
12 'xcolumn','x',2,'numeric',
13 'lcolumn','l',2,'numeric',
14 'factor1','f1',2,'numeric',
15 'factor2','f2',1,'numeric',
16 'outdir','o',2,'character',
17 'htmlfile','h',2,'character'
18 ),byrow=TRUE,ncol=4);
19
20
21 options <- getopt(option_specification);
22 options(bitmapType="cairo")
23
24
25
26 if (!is.null(options$outdir)) {
27 # Create the directory
28 dir.create(options$outdir,FALSE)
29 }
30
31
32 galaxy_biom <- import_biom(options$biomfile)
33 galaxy_map <- import_qiime_sample_data(options$metafile)
34
35
36 tax_col_norm <- c("Kingdom","Phylum","Class","Order","Family","Genus","Species")
37 tax_col_extra <- c("None","Kingdom","Phylum","Class","Order","Family","Genus","Species")
38
39 number.of.tax.rank<-length(colnames(tax_table(galaxy_biom)))
40
41 if( number.of.tax.rank == 7){
42 colnames(tax_table(galaxy_biom)) <- tax_col_norm
43 }else{
44 colnames(tax_table(galaxy_biom)) <- tax_col_extra
45 }
46
47
48 AIP_galaxy <- merge_phyloseq(galaxy_biom,galaxy_map)
49
50
51 pdffile <- gsub("[ ]+", "", paste(options$outdir,"/abundance.pdf"))
52 pngfile_abundance <- gsub("[ ]+", "", paste(options$outdir,"/abundance.png"))
53 htmlfile <- gsub("[ ]+", "", paste(options$htmlfile))
54
55
56 ###### To obtain the column name in metadata ################
57 x.selectedColumn<-colnames(galaxy_map)[options$xcolumn]
58 l.selectedColumn<-colnames(galaxy_map)[options$lcolumn]
59 f1.selectedColumn<-colnames(galaxy_map)[options$factor1]
60
61 factor.var <- f1.selectedColumn
62
63 if(!is.null(options$factor2)){
64 f2.selectedColumn<-colnames(galaxy_map)[options$factor2]
65 factor.var <- paste(f1.selectedColumn,f2.selectedColumn,sep="+")
66 }
67
68
69 # Produce PDF file
70 pdf(pdffile);
71 plot_bar(AIP_galaxy,x=x.selectedColumn,facet_grid = paste('~', factor.var),fill=l.selectedColumn)
72 garbage<-dev.off();
73
74 #png('abundance_1.png')
75 bitmap(pngfile_abundance,"png16m")
76 plot_bar(AIP_galaxy,x=x.selectedColumn,facet_grid = paste('~', factor.var),fill=l.selectedColumn)
77 garbage<-dev.off()
78
79 # Produce the HTML file
80 htmlfile_handle <- file(htmlfile)
81 html_output = c('<html><body>',
82 '<table align="center">',
83 '<tr>',
84 '<td valign="middle" style="vertical-align:middle;">',
85 '<a href="abundance.pdf"><img src="abundance.png"/></a>',
86 '</td>',
87 '</tr>',
88 '</table>',
89 '</html></body>');
90 writeLines(html_output, htmlfile_handle);
91 close(htmlfile_handle);