Mercurial > repos > artbio > gsc_correlation

annotate correlation_with_signature.R @ 0:6f3da989b59d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
author artbio
date Mon, 24 Jun 2019 07:18:35 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
1 # Performs multi-correlation analysis between the vectors of gene expressions
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
2 # in single cell RNAseq libraries and the vectors of signature scores in these
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
3 # same single cell RNAseq libraries.
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
4
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
5 # Example of command
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
6 # Rscript correlations_with_signature.R --expression_file <expression_data.tsv>
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
7 # --signatures_file <signature_scores.tsv>
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
8 # --sep "\t"
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
9 # --colnames "T"
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
10 # --gene_corr <gene-gene corr file>
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
11 # --gene_corr_pval <gene-gene corr pvalues file>
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
12 # --sig_corr <genes correlation to signature file>
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
13
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
14 # load packages that are provided in the conda env
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
15 options( show.error.messages=F,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
16 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
17 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
18 requiredPackages = c('optparse', 'Hmisc')
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
19 warnings()
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
20
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
21 library(optparse)
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
22 library(Hmisc)
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
23
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
24 # Arguments
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
25 option_list = list(
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
26 make_option(
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
27 "--sep",
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
28 default = '\t',
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
29 type = 'character',
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
30 help = "File separator, must be the same for all input files [default : '%default' ]"
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
31 ),
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
32 make_option(
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
33 "--colnames",
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
34 default = TRUE,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
35 type = 'logical',
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
36 help = "Consider first lines as header (must stand for all input files) [default : '%default' ]"
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
37 ),
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
38 make_option(
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
39 "--expression_file",
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
40 default = NA,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
41 type = 'character',
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
42 help = "Input file that contains log2(CPM +1) expression values"
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
43 ),
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
44 make_option(
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
45 "--signatures_file",
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
46 default = NA,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
47 type = 'character',
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
48 help = "Input file that contains cell signature"
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
49 ),
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
50 make_option(
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
51 "--sig_corr",
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
52 default = "sig_corr.tsv",
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
53 type = 'character',
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
54 help = "signature correlations output [default : '%default' ]"
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
55 ),
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
56 make_option(
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
57 "--gene_corr",
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
58 default = "gene_corr.tsv",
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
59 type = 'character',
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
60 help = "genes-genes correlations output [default : '%default' ]"
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
61 ),
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
62 make_option(
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
63 "--gene_corr_pval",
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
64 default = "gene_corr_pval.tsv",
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
65 type = 'character',
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
66 help = "genes-genes correlations pvalues output [default : '%default' ]"
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
67 )
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
68 )
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
69
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
70 opt = parse_args(OptionParser(option_list = option_list),
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
71 args = commandArgs(trailingOnly = TRUE))
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
72
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
73 if (opt$sep == "tab") {opt$sep = "\t"}
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
74 if (opt$sep == "comma") {opt$sep = ","}
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
75
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
76 # Open files
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
77 data <- read.table(
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
78 opt$expression_file,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
79 header = opt$colnames,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
80 row.names = 1,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
81 sep = opt$sep,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
82 check.names = F
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
83 )
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
84 signature <- read.delim(
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
85 opt$signatures_file,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
86 header = T,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
87 stringsAsFactors = F,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
88 row.names = 1,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
89 sep = opt$sep,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
90 check.names = F
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
91 )
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
92
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
93
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
94 # keep only signatures that are in the expression dataframe
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
95 signature <- subset(signature, rownames(signature) %in% colnames(data))
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
96
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
97 # Add signature score to expression matrix
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
98 data <- rbind(t(signature), data)
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
99
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
100 # Gene correlation
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
101 gene_corr <- rcorr(t(data), type = "pearson") # transpose because we correlate genes, not cells
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
102
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
103 # Gene correlation with signature score
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
104 gene_signature_corr <- cbind.data.frame(gene = colnames(gene_corr$r),
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
105 Pearson_correlation = gene_corr$r[, 1],
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
106 p_value = gene_corr$P[, 1])
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
107 gene_signature_corr <- gene_signature_corr[ order(gene_signature_corr[,2], decreasing = T), ]
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
108
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
109
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
110 # Save files
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
111 write.table(
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
112 gene_signature_corr,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
113 file = opt$sig_corr,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
114 sep = "\t",
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
115 quote = F,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
116 col.names = T,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
117 row.names = F
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
118 )
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
119
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
120 r_genes <- data.frame(gene=rownames(gene_corr$r), gene_corr$r) # add rownames as a variable for output
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
121 p_genes <- data.frame(gene=rownames(gene_corr$P), gene_corr$P) # add rownames as a variable for output
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
122 write.table(
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
123 r_genes[-1,-2],
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
124 file = opt$gene_corr,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
125 sep = "\t",
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
126 quote = F,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
127 col.names = T,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
128 row.names = F
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
129 )
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
130 write.table(
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
131 p_genes[-1,-2],
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
132 file = opt$gene_corr_pval,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
133 sep = "\t",
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
134 quote = F,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
135 col.names = T,
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
136 row.names = F
6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
artbio
parents:
diff changeset
137 )