edger: edger.R annotate

annotate edger.R @ 15:5bf899c13979 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2

author	iuc
date	Wed, 22 Nov 2023 03:57:37 +0000
parents	070900306913
children

rev	line source
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1 # This tool takes in a matrix of feature counts as well as gene annotations and
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	2 # outputs a table of top expressions as well as various plots for differential
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	3 # expression analysis
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	4 #
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	5 # ARGS: htmlPath", "R", 1, "character" -Path to html file linking to other outputs
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	6 # outPath", "o", 1, "character" -Path to folder to write all output to
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	7 # filesPath", "j", 2, "character" -JSON list object if multiple files input
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	8 # matrixPath", "m", 2, "character" -Path to count matrix
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	9 # factFile", "f", 2, "character" -Path to factor information file
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	10 # factInput", "i", 2, "character" -String containing factors if manually input
14 070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	11 # formula", "F", 2, "character". -String containing a formula to override default use of factInput
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	12 # annoPath", "a", 2, "character" -Path to input containing gene annotations
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	13 # contrastData", "C", 1, "character" -String containing contrasts of interest
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	14 # cpmReq", "c", 2, "double" -Float specifying cpm requirement
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	15 # cntReq", "z", 2, "integer" -Integer specifying minimum total count requirement
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	16 # sampleReq", "s", 2, "integer" -Integer specifying cpm requirement
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	17 # normCounts", "x", 0, "logical" -String specifying if normalised counts should be output
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	18 # rdaOpt", "r", 0, "logical" -String specifying if RData should be output
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	19 # lfcReq", "l", 1, "double" -Float specifying the log-fold-change requirement
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	20 # pValReq", "p", 1, "double" -Float specifying the p-value requirement
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	21 # pAdjOpt", "d", 1, "character" -String specifying the p-value adjustment method
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	22 # normOpt", "n", 1, "character" -String specifying type of normalisation used
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	23 # robOpt", "b", 0, "logical" -String specifying if robust options should be used
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	24 # lrtOpt", "t", 0, "logical" -String specifying whether to perform LRT test instead
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	25 #
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	26 # OUT:
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	27 # MDS Plot
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	28 # BCV Plot
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	29 # QL Plot
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	30 # MD Plot
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	31 # Expression Table
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	32 # HTML file linking to the ouputs
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	33 # Optional:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	34 # Normalised counts Table
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	35 # RData file
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	36 #
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	37 # Author: Shian Su - registertonysu@gmail.com - Jan 2014
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	38 # Modified by: Maria Doyle - Oct 2017 (some code taken from the DESeq2 wrapper)
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	39
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	40 # Record starting time
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	41 time_start <- as.character(Sys.time())
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	42
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	43 # setup R error handling to go to stderr
12 a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 9 diff changeset	44 options(show.error.messages = FALSE, error = function() {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	45 cat(geterrmessage(), file = stderr())
12 a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 9 diff changeset	46 q("no", 1, FALSE)
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	47 })
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	48
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	49 # we need that to not crash galaxy with an UTF8 error on German LC settings.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	50 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	51
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	52 # Load all required libraries
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	53 library(methods, quietly = TRUE, warn.conflicts = FALSE)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	54 library(statmod, quietly = TRUE, warn.conflicts = FALSE)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	55 library(splines, quietly = TRUE, warn.conflicts = FALSE)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	56 library(edgeR, quietly = TRUE, warn.conflicts = FALSE)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	57 library(limma, quietly = TRUE, warn.conflicts = FALSE)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	58 library(scales, quietly = TRUE, warn.conflicts = FALSE)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	59 library(getopt, quietly = TRUE, warn.conflicts = FALSE)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	60
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	61 ################################################################################
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	62 ### Function Delcaration
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	63 ################################################################################
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	64 # Function to sanitise contrast equations so there are no whitespaces
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	65 # surrounding the arithmetic operators, leading or trailing whitespace
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	66 sanitise_equation <- function(equation) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	67 equation <- gsub(" [+] ", "+", equation)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	68 equation <- gsub(" [-] ", "-", equation)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	69 equation <- gsub(" [/] ", "/", equation)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	70 equation <- gsub(" [] ", "", equation)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	71 equation <- gsub("^\\s+\|\\s+$", "", equation)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	72 return(equation)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	73 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	74
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	75 # Function to sanitise group information
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	76 sanitise_groups <- function(string) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	77 string <- gsub(" [,] ", ",", string)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	78 string <- gsub("^\\s+\|\\s+$", "", string)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	79 return(string)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	80 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	81
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	82 # Function to change periods to whitespace in a string
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	83 unmake_names <- function(string) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	84 string <- gsub(".", " ", string, fixed = TRUE)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	85 return(string)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	86 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	87
15 5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	88 # Sanitise file base names coming from factors or contrasts
5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	89 sanitise_basename <- function(string) {
5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	90 string <- gsub("[/^]", "_", string)
5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	91 return(string)
5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	92 }
5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	93
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	94 # Generate output folder and paths
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	95 make_out <- function(filename) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	96 return(paste0(out_path, "/", filename))
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	97 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	98
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	99 # Generating design information
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	100 paste_listname <- function(string) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	101 return(paste0("factors$", string))
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	102 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	103
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	104 # Create cata function: default path set, default seperator empty and appending
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	105 # true by default (Ripped straight from the cat function with altered argument
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	106 # defaults)
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	107 cata <- function(..., file = opt$htmlPath, sep = "", fill = FALSE, labels = NULL,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	108 append = TRUE) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	109 if (is.character(file)) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	110 if (file == "") {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	111 file <- stdout()
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	112 } else if (substring(file, 1L, 1L) == "\|") {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	113 file <- pipe(substring(file, 2L), "w")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	114 on.exit(close(file))
12 a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 9 diff changeset	115 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	116 file <- file(file, ifelse(append, "a", "w"))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	117 on.exit(close(file))
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	118 }
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	119 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	120 .Internal(cat(list(...), file, sep, fill, labels, append))
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	121 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	122
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	123 # Function to write code for html head and title
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	124 html_head <- function(title) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	125 cata("<head>\n")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	126 cata("<title>", title, "</title>\n")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	127 cata("</head>\n")
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	128 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	129
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	130 # Function to write code for html links
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	131 html_link <- function(address, label = address) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	132 cata("<a href=\"", address, "\" target=\"_blank\">", label, "</a><br />\n")
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	133 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	134
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	135 # Function to write code for html images
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	136 html_image <- function(source, label = source, height = 600, width = 600) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	137 cata("<img src=\"", source, "\" alt=\"", label, "\" height=\"", height)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	138 cata("\" width=\"", width, "\"/>\n")
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	139 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	140
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	141 # Function to write code for html list items
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	142 list_item <- function(...) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	143 cata("<li>", ..., "</li>\n")
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	144 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	145
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	146 table_item <- function(...) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	147 cata("<td>", ..., "</td>\n")
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	148 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	149
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	150 table_head_item <- function(...) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	151 cata("<th>", ..., "</th>\n")
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	152 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	153
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	154 ################################################################################
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	155 ### Input Processing
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	156 ################################################################################
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	157
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	158 # Collect arguments from command line
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	159 args <- commandArgs(trailingOnly = TRUE)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	160
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	161 # Get options, using the spec as defined by the enclosed list.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	162 # Read the options from the default: commandArgs(TRUE).
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	163 spec <- matrix(c(
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	164 "htmlPath", "R", 1, "character",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	165 "outPath", "o", 1, "character",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	166 "filesPath", "j", 2, "character",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	167 "matrixPath", "m", 2, "character",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	168 "factFile", "f", 2, "character",
14 070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	169 "formula", "F", 2, "character",
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	170 "factInput", "i", 2, "character",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	171 "annoPath", "a", 2, "character",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	172 "contrastData", "C", 1, "character",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	173 "cpmReq", "c", 1, "double",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	174 "totReq", "y", 0, "logical",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	175 "cntReq", "z", 1, "integer",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	176 "sampleReq", "s", 1, "integer",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	177 "normCounts", "x", 0, "logical",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	178 "rdaOpt", "r", 0, "logical",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	179 "lfcReq", "l", 1, "double",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	180 "pValReq", "p", 1, "double",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	181 "pAdjOpt", "d", 1, "character",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	182 "normOpt", "n", 1, "character",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	183 "robOpt", "b", 0, "logical",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	184 "lrtOpt", "t", 0, "logical"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	185 ),
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	186 byrow = TRUE, ncol = 4
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	187 )
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	188 opt <- getopt(spec)
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	189
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	190
12 a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 9 diff changeset	191 if (is.null(opt$matrixPath) && is.null(opt$filesPath)) {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	192 cat("A counts matrix (or a set of counts files) is required.\n")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	193 q(status = 1)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	194 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	195
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	196 if (is.null(opt$cpmReq)) {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	197 filt_cpm <- FALSE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	198 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	199 filt_cpm <- TRUE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	200 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	201
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	202 if (is.null(opt$cntReq) \|\| is.null(opt$sampleReq)) {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	203 filt_smpcount <- FALSE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	204 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	205 filt_smpcount <- TRUE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	206 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	207
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	208 if (is.null(opt$totReq)) {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	209 filt_totcount <- FALSE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	210 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	211 filt_totcount <- TRUE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	212 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	213
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	214 if (is.null(opt$lrtOpt)) {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	215 want_lrt <- FALSE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	216 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	217 want_lrt <- TRUE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	218 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	219
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	220 if (is.null(opt$rdaOpt)) {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	221 want_rda <- FALSE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	222 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	223 want_rda <- TRUE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	224 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	225
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	226 if (is.null(opt$annoPath)) {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	227 have_anno <- FALSE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	228 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	229 have_anno <- TRUE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	230 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	231
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	232 if (is.null(opt$normCounts)) {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	233 want_norm <- FALSE
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	234 } else {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	235 want_norm <- TRUE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	236 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	237
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	238 if (is.null(opt$robOpt)) {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	239 want_robust <- FALSE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	240 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	241 want_robust <- TRUE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	242 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	243
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	244
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	245 if (!is.null(opt$filesPath)) {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	246 # Process the separate count files (adapted from DESeq2 wrapper)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	247 library("rjson")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	248 parser <- newJSONParser()
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	249 parser$addData(opt$filesPath)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	250 factor_list <- parser$getObject()
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	251 factors <- sapply(factor_list, function(x) x[[1]])
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	252 filenames_in <- unname(unlist(factor_list[[1]][[2]]))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	253 sampletable <- data.frame(
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	254 sample = basename(filenames_in),
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	255 filename = filenames_in,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	256 row.names = filenames_in,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	257 stringsAsFactors = FALSE
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	258 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	259 for (factor in factor_list) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	260 factorname <- factor[[1]]
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	261 sampletable[[factorname]] <- character(nrow(sampletable))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	262 lvls <- sapply(factor[[2]], function(x) names(x))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	263 for (i in seq_along(factor[[2]])) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	264 files <- factor[[2]][[i]][[1]]
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	265 sampletable[files, factorname] <- lvls[i]
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	266 }
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	267 sampletable[[factorname]] <- factor(sampletable[[factorname]], levels = lvls)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	268 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	269 rownames(sampletable) <- sampletable$sample
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	270 rem <- c("sample", "filename")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	271 factors <- sampletable[, !(names(sampletable) %in% rem), drop = FALSE]
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	272
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	273 # read in count files and create single table
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	274 countfiles <- lapply(sampletable$filename, function(x) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	275 read.delim(x, row.names = 1)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	276 })
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	277 counts <- do.call("cbind", countfiles)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	278 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	279 # Process the single count matrix
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	280 counts <- read.table(opt$matrixPath, header = TRUE, sep = "\t", strip.white = TRUE, stringsAsFactors = FALSE)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	281 row.names(counts) <- counts[, 1]
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	282 counts <- counts[, -1]
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	283 countsrows <- nrow(counts)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	284
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	285 # Process factors
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	286 if (is.null(opt$factInput)) {
9 6e53e565fc6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 8c4b8f8711df0a4d6fa98fa8a6f91b977395d62c" iuc parents: 8 diff changeset	287 factordata <- read.table(opt$factFile, header = TRUE, sep = "\t", strip.white = TRUE, stringsAsFactors = TRUE)
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	288 # check samples names match
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	289 if (!any(factordata[, 1] %in% colnames(counts))) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	290 stop("Sample IDs in factors file and count matrix don't match")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	291 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	292 # order samples as in counts matrix
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	293 factordata <- factordata[match(colnames(counts), factordata[, 1]), ]
13 0cb907a2a810 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 95a36f5b0bd139f161d131b4c2c9c36940e749c6 iuc parents: 12 diff changeset	294 factors <- data.frame(sapply(factordata[, -1, drop = FALSE], make.names))
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	295 } else {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	296 factors <- unlist(strsplit(opt$factInput, "\|", fixed = TRUE))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	297 factordata <- list()
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	298 for (fact in factors) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	299 newfact <- unlist(strsplit(fact, split = "::"))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	300 factordata <- rbind(factordata, newfact)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	301 } # Factors have the form: FACT_NAME::LEVEL,LEVEL,LEVEL,LEVEL,... The first factor is the Primary Factor.
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	302
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	303 # Set the row names to be the name of the factor and delete first row
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	304 row.names(factordata) <- factordata[, 1]
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	305 factordata <- factordata[, -1]
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	306 factordata <- sapply(factordata, sanitise_groups)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	307 factordata <- sapply(factordata, strsplit, split = ",")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	308 factordata <- sapply(factordata, make.names)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	309 # Transform factor data into data frame of R factor objects
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	310 factors <- data.frame(factordata)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	311 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	312 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	313
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	314 # if annotation file provided
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	315 if (have_anno) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	316 geneanno <- read.table(opt$annoPath, header = TRUE, sep = "\t", quote = "", strip.white = TRUE, stringsAsFactors = FALSE)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	317 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	318
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	319 # Create output directory
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	320 out_path <- opt$outPath
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	321 dir.create(out_path, showWarnings = FALSE)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	322
14 070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	323 # Check if contrastData is a file or not
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	324 if (file.exists(opt$contrastData)) {
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	325 contrast_data <- unlist(read.table(opt$contrastData, sep = "\t", header = TRUE)[[1]])
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	326 } else {
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	327 # Split up contrasts separated by comma into a vector then sanitise
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	328 contrast_data <- unlist(strsplit(opt$contrastData, split = ","))
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	329 }
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	330 contrast_data <- sanitise_equation(contrast_data)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	331 contrast_data <- gsub(" ", ".", contrast_data, fixed = TRUE)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	332
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	333 bcv_pdf <- make_out("bcvplot.pdf")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	334 bcv_png <- make_out("bcvplot.png")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	335 ql_pdf <- make_out("qlplot.pdf")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	336 ql_png <- make_out("qlplot.png")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	337 mds_pdf <- character() # Initialise character vector
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	338 mds_png <- character()
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	339 for (i in seq_len(ncol(factors))) {
15 5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	340 mds_pdf[i] <- make_out(paste0("mdsplot_", sanitise_basename(names(factors)[i]), ".pdf"))
5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	341 mds_png[i] <- make_out(paste0("mdsplot_", sanitise_basename(names(factors)[i]), ".png"))
3 d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	342 }
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	343 md_pdf <- character()
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	344 md_png <- character()
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	345 top_out <- character()
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	346 for (i in seq_along(contrast_data)) {
15 5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	347 md_pdf[i] <- make_out(paste0("mdplot_", sanitise_basename(contrast_data[i]), ".pdf"))
5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	348 md_png[i] <- make_out(paste0("mdplot_", sanitise_basename(contrast_data[i]), ".png"))
5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	349 top_out[i] <- make_out(paste0("edgeR_", sanitise_basename(contrast_data[i]), ".tsv"))
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	350 } # Save output paths for each contrast as vectors
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	351 norm_out <- make_out("edgeR_normcounts.tsv")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	352 rda_out <- make_out("edgeR_analysis.RData")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	353 session_out <- make_out("session_info.txt")
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	354
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	355 # Initialise data for html links and images, data frame with columns Label and
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	356 # Link
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	357 link_data <- data.frame(Label = character(), Link = character(), stringsAsFactors = FALSE)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	358 image_data <- data.frame(Label = character(), Link = character(), stringsAsFactors = FALSE)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	359
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	360 # Initialise vectors for storage of up/down/neutral regulated counts
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	361 up_count <- numeric()
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	362 down_count <- numeric()
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	363 flat_count <- numeric()
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	364
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	365 ################################################################################
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	366 ### Data Processing
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	367 ################################################################################
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	368
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	369 # Extract counts and annotation data
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	370 data <- list()
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	371 data$counts <- counts
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	372 if (have_anno) {
3 d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	373 # order annotation by genes in counts (assumes gene ids are in 1st column of geneanno)
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	374 annoord <- geneanno[match(row.names(counts), geneanno[, 1]), ]
3 d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	375 data$genes <- annoord
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	376 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	377 data$genes <- data.frame(GeneID = row.names(counts))
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	378 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	379
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	380 # If filter crieteria set, filter out genes that do not have a required cpm/counts in a required number of
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	381 # samples. Default is no filtering
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	382 prefilter_count <- nrow(data$counts)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	383
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	384 if (filt_cpm \|\| filt_smpcount \|\| filt_totcount) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	385 if (filt_totcount) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	386 keep <- rowSums(data$counts) >= opt$cntReq
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	387 } else if (filt_smpcount) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	388 keep <- rowSums(data$counts >= opt$cntReq) >= opt$sampleReq
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	389 } else if (filt_cpm) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	390 keep <- rowSums(cpm(data$counts) >= opt$cpmReq) >= opt$sampleReq
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	391 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	392
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	393 data$counts <- data$counts[keep, ]
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	394 data$genes <- data$genes[keep, , drop = FALSE]
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	395 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	396
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	397 postfilter_count <- nrow(data$counts)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	398 filtered_count <- prefilter_count - postfilter_count
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	399
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	400 # Name rows of factors according to their sample
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	401 row.names(factors) <- names(data$counts)
12 a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 9 diff changeset	402 factor_list <- names(factors)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	403
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	404 # Generating the DGEList object "data"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	405 samplenames <- colnames(data$counts)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	406 genes <- data$genes
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	407 data <- DGEList(data$counts)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	408 colnames(data) <- samplenames
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	409 data$samples <- factors
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	410 data$genes <- genes
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	411
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	412
14 070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	413 if (!is.null(opt$formula)) {
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	414 formula <- opt$formula
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	415 # sanitisation can be getting rid of the "~"
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	416 if (!startsWith(formula, "~")) {
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	417 formula <- paste0("~", formula)
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	418 }
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	419 } else {
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	420 formula <- "~0"
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	421 for (i in seq_along(factor_list)) {
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	422 formula <- paste(formula, factor_list[i], sep = "+")
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	423 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	424 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	425
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	426 formula <- formula(formula)
12 a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 9 diff changeset	427 design <- model.matrix(formula, factors)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	428
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	429 for (i in seq_along(factor_list)) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	430 colnames(design) <- gsub(factor_list[i], "", colnames(design), fixed = TRUE)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	431 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	432
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	433 # Calculating normalising factor, estimating dispersion
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	434 data <- calcNormFactors(data, method = opt$normOpt)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	435
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	436 if (want_robust) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	437 data <- estimateDisp(data, design = design, robust = TRUE)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	438 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	439 data <- estimateDisp(data, design = design)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	440 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	441
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	442 # Generate contrasts information
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	443 contrasts <- makeContrasts(contrasts = contrast_data, levels = design)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	444
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	445 ################################################################################
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	446 ### Data Output
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	447 ################################################################################
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	448
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	449 # Plot MDS
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	450 labels <- names(counts)
3 d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	451
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	452 # MDS plot
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	453 png(mds_png, width = 600, height = 600)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	454 plotMDS(data, labels = labels, col = as.numeric(factors[, 1]), cex = 0.8, main = paste("MDS Plot:", names(factors)[1]))
15 5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	455 img_name <- paste0("MDS Plot_", sanitise_basename(names(factors)[1]), ".png")
5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	456 img_addr <- paste0("mdsplot_", sanitise_basename(names(factors)[1]), ".png")
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	457 image_data[1, ] <- c(img_name, img_addr)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	458 invisible(dev.off())
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	459
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	460 pdf(mds_pdf)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	461 plotMDS(data, labels = labels, col = as.numeric(factors[, 1]), cex = 0.8, main = paste("MDS Plot:", names(factors)[1]))
15 5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	462 link_name <- paste0("MDS Plot_", sanitise_basename(names(factors)[1]), ".pdf")
5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	463 link_addr <- paste0("mdsplot_", sanitise_basename(names(factors)[1]), ".pdf")
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	464 link_data[1, ] <- c(link_name, link_addr)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	465 invisible(dev.off())
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	466
3 d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	467 # If additional factors create additional MDS plots coloured by factor
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	468 if (ncol(factors) > 1) {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	469 for (i in 2:ncol(factors)) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	470 png(mds_png[i], width = 600, height = 600)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	471 plotMDS(data, labels = labels, col = as.numeric(factors[, i]), cex = 0.8, main = paste("MDS Plot:", names(factors)[i]))
15 5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	472 img_name <- paste0("MDS Plot_", sanitise_basename(names(factors)[i]), ".png")
5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	473 img_addr <- paste0("mdsplot_", sanitise_basename(names(factors)[i]), ".png")
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	474 image_data <- rbind(image_data, c(img_name, img_addr))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	475 invisible(dev.off())
3 d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	476
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	477 pdf(mds_pdf[i])
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	478 plotMDS(data, labels = labels, col = as.numeric(factors[, i]), cex = 0.8, main = paste("MDS Plot:", names(factors)[i]))
15 5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	479 link_name <- paste0("MDS Plot_", sanitise_basename(names(factors)[i]), ".pdf")
5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	480 link_addr <- paste0("mdsplot_", sanitise_basename(names(factors)[i]), ".pdf")
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	481 link_data <- rbind(link_data, c(link_name, link_addr))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	482 invisible(dev.off())
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	483 }
3 d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	484 }
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	485
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	486 # BCV Plot
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	487 png(bcv_png, width = 600, height = 600)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	488 plotBCV(data, main = "BCV Plot")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	489 img_name <- "BCV Plot"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	490 img_addr <- "bcvplot.png"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	491 image_data <- rbind(image_data, c(img_name, img_addr))
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	492 invisible(dev.off())
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	493
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	494 pdf(bcv_pdf)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	495 plotBCV(data, main = "BCV Plot")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	496 link_name <- paste0("BCV Plot.pdf")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	497 link_addr <- paste0("bcvplot.pdf")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	498 link_data <- rbind(link_data, c(link_name, link_addr))
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	499 invisible(dev.off())
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	500
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	501 # Generate fit
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	502 if (want_lrt) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	503 fit <- glmFit(data, design)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	504 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	505 if (want_robust) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	506 fit <- glmQLFit(data, design, robust = TRUE)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	507 } else {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	508 fit <- glmQLFit(data, design)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	509 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	510
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	511 # Plot QL dispersions
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	512 png(ql_png, width = 600, height = 600)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	513 plotQLDisp(fit, main = "QL Plot")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	514 img_name <- "QL Plot"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	515 img_addr <- "qlplot.png"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	516 image_data <- rbind(image_data, c(img_name, img_addr))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	517 invisible(dev.off())
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	518
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	519 pdf(ql_pdf)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	520 plotQLDisp(fit, main = "QL Plot")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	521 link_name <- "QL Plot.pdf"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	522 link_addr <- "qlplot.pdf"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	523 link_data <- rbind(link_data, c(link_name, link_addr))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	524 invisible(dev.off())
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	525 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	526
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	527 # Save normalised counts (log2cpm)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	528 if (want_norm) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	529 normalised_counts <- cpm(data, normalized.lib.sizes = TRUE, log = TRUE)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	530 normalised_counts <- data.frame(data$genes, normalised_counts)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	531 write.table(normalised_counts, file = norm_out, row.names = FALSE, sep = "\t", quote = FALSE)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	532 link_data <- rbind(link_data, c("edgeR_normcounts.tsv", "edgeR_normcounts.tsv"))
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	533 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	534
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	535
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	536 for (i in seq_along(contrast_data)) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	537 if (want_lrt) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	538 res <- glmLRT(fit, contrast = contrasts[, i])
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	539 } else {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	540 res <- glmQLFTest(fit, contrast = contrasts[, i])
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	541 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	542
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	543 status <- decideTestsDGE(res,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	544 adjust.method = opt$pAdjOpt, p.value = opt$pValReq,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	545 lfc = opt$lfcReq
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	546 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	547 sum_status <- summary(status)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	548
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	549 # Collect counts for differential expression
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	550 up_count[i] <- sum_status["Up", ]
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	551 down_count[i] <- sum_status["Down", ]
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	552 flat_count[i] <- sum_status["NotSig", ]
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	553
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	554 # Write top expressions table
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	555 top <- topTags(res, adjust.method = opt$pAdjOpt, n = Inf, sort.by = "PValue")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	556 write.table(top, file = top_out[i], row.names = FALSE, sep = "\t", quote = FALSE)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	557
15 5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	558 link_name <- paste0("edgeR_", sanitise_basename(contrast_data[i]), ".tsv")
5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	559 link_addr <- paste0("edgeR_", sanitise_basename(contrast_data[i]), ".tsv")
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	560 link_data <- rbind(link_data, c(link_name, link_addr))
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	561
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	562 # Plot MD (log ratios vs mean difference) using limma package
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	563 pdf(md_pdf[i])
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	564 limma::plotMD(res,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	565 status = status,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	566 main = paste("MD Plot:", unmake_names(contrast_data[i])),
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	567 hl.col = alpha(c("firebrick", "blue"), 0.4), values = c(1, -1),
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	568 xlab = "Average Expression", ylab = "logFC"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	569 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	570
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	571 abline(h = 0, col = "grey", lty = 2)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	572
15 5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	573 link_name <- paste0("MD Plot_", sanitise_basename(contrast_data[i]), ".pdf")
5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	574 link_addr <- paste0("mdplot_", sanitise_basename(contrast_data[i]), ".pdf")
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	575 link_data <- rbind(link_data, c(link_name, link_addr))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	576 invisible(dev.off())
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	577
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	578 png(md_png[i], height = 600, width = 600)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	579 limma::plotMD(res,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	580 status = status,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	581 main = paste("MD Plot:", unmake_names(contrast_data[i])),
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	582 hl.col = alpha(c("firebrick", "blue"), 0.4), values = c(1, -1),
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	583 xlab = "Average Expression", ylab = "logFC"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	584 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	585
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	586 abline(h = 0, col = "grey", lty = 2)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	587
15 5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	588 img_name <- paste0("MD Plot_", sanitise_basename(contrast_data[i]), ".png")
5bf899c13979 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 025a0d70be99e50ae89ad78a70cc8c51571ea1a2 iuc parents: 14 diff changeset	589 img_addr <- paste0("mdplot_", sanitise_basename(contrast_data[i]), ".png")
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	590 image_data <- rbind(image_data, c(img_name, img_addr))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	591 invisible(dev.off())
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	592 }
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	593 sig_diff <- data.frame(Up = up_count, Flat = flat_count, Down = down_count)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	594 row.names(sig_diff) <- contrast_data
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	595
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	596 # Save relevant items as rda object
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	597 if (want_rda) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	598 if (want_norm) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	599 save(counts, data, status, normalised_counts, labels, factors, fit, res, top, contrasts, design,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	600 file = rda_out, ascii = TRUE
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	601 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	602 } else {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	603 save(counts, data, status, labels, factors, fit, res, top, contrasts, design,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	604 file = rda_out, ascii = TRUE
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	605 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	606 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	607 link_data <- rbind(link_data, c("edgeR_analysis.RData", "edgeR_analysis.RData"))
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	608 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	609
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	610 # Record session info
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	611 writeLines(capture.output(sessionInfo()), session_out)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	612 link_data <- rbind(link_data, c("Session Info", "session_info.txt"))
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	613
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	614 # Record ending time and calculate total run time
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	615 time_end <- as.character(Sys.time())
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	616 time_taken <- capture.output(round(difftime(time_end, time_start), digits = 3))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	617 time_taken <- gsub("Time difference of ", "", time_taken, fixed = TRUE)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	618
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	619 ################################################################################
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	620 ### HTML Generation
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	621 ################################################################################
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	622
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	623 # Clear file
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	624 cat("", file = opt$htmlPath)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	625
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	626 cata("<html>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	627
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	628 cata("<body>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	629 cata("<h3>edgeR Analysis Output:</h3>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	630 cata("Links to PDF copies of plots are in 'Plots' section below.<br />\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	631
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	632 html_image(image_data$Link[1], image_data$Label[1])
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	633
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	634 for (i in 2:nrow(image_data)) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	635 html_image(image_data$Link[i], image_data$Label[i])
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	636 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	637
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	638 cata("<h4>Differential Expression Counts:</h4>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	639
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	640 cata("<table border=\"1\" cellpadding=\"4\">\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	641 cata("<tr>\n")
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	642 table_item()
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	643 for (i in colnames(sig_diff)) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	644 table_head_item(i)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	645 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	646 cata("</tr>\n")
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	647 for (i in seq_len(nrow(sig_diff))) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	648 cata("<tr>\n")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	649 table_head_item(unmake_names(row.names(sig_diff)[i]))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	650 for (j in seq_len(ncol(sig_diff))) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	651 table_item(as.character(sig_diff[i, j]))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	652 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	653 cata("</tr>\n")
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	654 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	655 cata("</table>")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	656
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	657 cata("<h4>Plots:</h4>\n")
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	658 for (i in seq_len(nrow(link_data))) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	659 if (grepl(".pdf", link_data$Link[i])) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	660 html_link(link_data$Link[i], link_data$Label[i])
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	661 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	662 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	663
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	664 cata("<h4>Tables:</h4>\n")
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	665 for (i in seq_len(nrow(link_data))) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	666 if (grepl(".tsv", link_data$Link[i])) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	667 html_link(link_data$Link[i], link_data$Label[i])
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	668 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	669 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	670
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	671 if (want_rda) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	672 cata("<h4>R Data Objects:</h4>\n")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	673 for (i in seq_len(nrow(link_data))) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	674 if (grepl(".RData", link_data$Link[i])) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	675 html_link(link_data$Link[i], link_data$Label[i])
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	676 }
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	677 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	678 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	679
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	680 cata("<p>Alt-click links to download file.</p>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	681 cata("<p>Click floppy disc icon associated history item to download ")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	682 cata("all files.</p>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	683 cata("<p>.tsv files can be viewed in Excel or any spreadsheet program.</p>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	684
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	685 cata("<h4>Additional Information</h4>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	686 cata("<ul>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	687
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	688 if (filt_cpm \|\| filt_smpcount \|\| filt_totcount) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	689 if (filt_cpm) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	690 temp_str <- paste(
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	691 "Genes without more than", opt$cpmReq,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	692 "CPM in at least", opt$sampleReq, "samples are insignificant",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	693 "and filtered out."
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	694 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	695 } else if (filt_smpcount) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	696 temp_str <- paste(
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	697 "Genes without more than", opt$cntReq,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	698 "counts in at least", opt$sampleReq, "samples are insignificant",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	699 "and filtered out."
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	700 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	701 } else if (filt_totcount) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	702 temp_str <- paste(
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	703 "Genes without more than", opt$cntReq,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	704 "counts, after summing counts for all samples, are insignificant",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	705 "and filtered out."
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	706 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	707 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	708
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	709 list_item(temp_str)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	710 filter_prop <- round(filtered_count / prefilter_count * 100, digits = 2)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	711 temp_str <- paste0(
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	712 filtered_count, " of ", prefilter_count, " (", filter_prop,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	713 "%) genes were filtered out for low expression."
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	714 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	715 list_item(temp_str)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	716 }
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	717 list_item(opt$normOpt, " was the method used to normalise library sizes.")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	718 if (want_lrt) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	719 list_item("The edgeR likelihood ratio test was used.")
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	720 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	721 if (want_robust) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	722 list_item("The edgeR quasi-likelihood test was used with robust settings (robust=TRUE with estimateDisp and glmQLFit).")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	723 } else {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	724 list_item("The edgeR quasi-likelihood test was used.")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	725 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	726 }
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	727 if (opt$pAdjOpt != "none") {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	728 if (opt$pAdjOpt == "BH" \|\| opt$pAdjOpt == "BY") {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	729 temp_str <- paste0(
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	730 "MD-Plot highlighted genes are significant at FDR ",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	731 "of ", opt$pValReq, " and exhibit log2-fold-change of at ",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	732 "least ", opt$lfcReq, "."
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	733 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	734 list_item(temp_str)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	735 } else if (opt$pAdjOpt == "holm") {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	736 temp_str <- paste0(
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	737 "MD-Plot highlighted genes are significant at adjusted ",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	738 "p-value of ", opt$pValReq, " by the Holm(1979) ",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	739 "method, and exhibit log2-fold-change of at least ",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	740 opt$lfcReq, "."
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	741 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	742 list_item(temp_str)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	743 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	744 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	745 temp_str <- paste0(
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	746 "MD-Plot highlighted genes are significant at p-value ",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	747 "of ", opt$pValReq, " and exhibit log2-fold-change of at ",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	748 "least ", opt$lfcReq, "."
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	749 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	750 list_item(temp_str)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	751 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	752 cata("</ul>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	753
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	754 cata("<h4>Summary of experimental data:</h4>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	755
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	756 cata("<p>CHECK THAT SAMPLES ARE ASSOCIATED WITH CORRECT GROUP(S)</p>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	757
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	758 cata("<table border=\"1\" cellpadding=\"3\">\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	759 cata("<tr>\n")
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	760 table_head_item("SampleID")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	761 table_head_item(names(factors)[1], " (Primary Factor)")
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	762
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	763 if (ncol(factors) > 1) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	764 for (i in names(factors)[2:length(names(factors))]) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	765 table_head_item(i)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	766 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	767 cata("</tr>\n")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	768 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	769
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	770 for (i in seq_len(nrow((factors)))) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	771 cata("<tr>\n")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	772 table_head_item(row.names(factors)[i])
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	773 for (j in seq_len(ncol(factors))) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	774 table_item(as.character(unmake_names(factors[i, j])))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	775 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	776 cata("</tr>\n")
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	777 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	778 cata("</table>")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	779
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	780 for (i in seq_len(nrow(link_data))) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	781 if (grepl("session_info", link_data$Link[i])) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	782 html_link(link_data$Link[i], link_data$Label[i])
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	783 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	784 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	785
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	786 cata("<table border=\"0\">\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	787 cata("<tr>\n")
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	788 table_item("Task started at:")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	789 table_item(time_start)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	790 cata("</tr>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	791 cata("<tr>\n")
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	792 table_item("Task ended at:")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	793 table_item(time_end)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	794 cata("</tr>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	795 cata("<tr>\n")
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	796 table_item("Task run time:")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	797 table_item(time_taken)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	798 cata("<tr>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	799 cata("</table>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	800
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	801 cata("</body>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	802 cata("</html>")

Mercurial > repos > iuc > edger

annotate edger.R @ 15:5bf899c13979 draft default tip