edger: edger.R annotate

annotate edger.R @ 14:070900306913 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774

author	iuc
date	Wed, 11 Oct 2023 11:13:07 +0000
parents	0cb907a2a810
children	5bf899c13979

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
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	88 # 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	89 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	90 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	91 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	92
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	93 # 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	94 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	95 return(paste0("factors$", string))
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	96 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	97
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	98 # Create cata function: default path set, default seperator empty and appending
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	99 # true by default (Ripped straight from the cat function with altered argument
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	100 # defaults)
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	101 cata <- function(..., file = opt$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	102 append = TRUE) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	103 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	104 if (file == "") {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	105 file <- stdout()
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	106 } 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	107 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	108 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	109 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	110 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	111 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	112 }
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	113 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	114 .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	115 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	116
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	117 # 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	118 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	119 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	120 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	121 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	122 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	123
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	124 # 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	125 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	126 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	127 }
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 # 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	130 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	131 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	132 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	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 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	136 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	137 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	138 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	139
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	140 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	141 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	142 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	143
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	144 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	145 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	146 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	147
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 ### Input Processing
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	150 ################################################################################
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	151
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	152 # 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	153 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	154
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	155 # 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	156 # 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	157 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	158 "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	159 "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	160 "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	161 "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	162 "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	163 "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	164 "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	165 "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	166 "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	167 "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	168 "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	169 "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	170 "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	171 "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	172 "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	173 "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	174 "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	175 "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	176 "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	177 "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	178 "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	179 ),
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	180 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	181 )
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	182 opt <- getopt(spec)
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	183
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	184
12 a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 9 diff changeset	185 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	186 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	187 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	188 }
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 if (is.null(opt$cpmReq)) {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	191 filt_cpm <- FALSE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	192 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	193 filt_cpm <- TRUE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	194 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	195
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	196 if (is.null(opt$cntReq) \|\| is.null(opt$sampleReq)) {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	197 filt_smpcount <- FALSE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	198 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	199 filt_smpcount <- TRUE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	200 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	201
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	202 if (is.null(opt$totReq)) {
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_totcount <- 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_totcount <- 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$lrtOpt)) {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	209 want_lrt <- FALSE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	210 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	211 want_lrt <- TRUE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	212 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	213
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	214 if (is.null(opt$rdaOpt)) {
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_rda <- 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_rda <- 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$annoPath)) {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	221 have_anno <- FALSE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	222 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	223 have_anno <- TRUE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	224 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	225
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	226 if (is.null(opt$normCounts)) {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	227 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	228 } else {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	229 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	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$robOpt)) {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	233 want_robust <- FALSE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	234 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	235 want_robust <- TRUE
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	236 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	237
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	238
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	239 if (!is.null(opt$filesPath)) {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	240 # 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	241 library("rjson")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	242 parser <- newJSONParser()
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	243 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	244 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	245 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	246 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	247 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	248 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	249 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	250 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	251 stringsAsFactors = FALSE
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	252 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	253 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	254 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	255 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	256 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	257 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	258 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	259 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	260 }
8 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]] <- 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	262 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	263 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	264 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	265 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	266
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	267 # 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	268 countfiles <- lapply(sampletable$filename, function(x) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	269 read.delim(x, row.names = 1)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	270 })
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	271 counts <- do.call("cbind", countfiles)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	272 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	273 # Process the single count matrix
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	274 counts <- read.table(opt$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	275 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	276 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	277 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	278
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 factors
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	280 if (is.null(opt$factInput)) {
9 6e53e565fc6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 8c4b8f8711df0a4d6fa98fa8a6f91b977395d62c" iuc parents: 8 diff changeset	281 factordata <- read.table(opt$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	282 # 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	283 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	284 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	285 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	286 # 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	287 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	288 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	289 } else {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	290 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	291 factordata <- list()
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	292 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	293 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	294 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	295 } # 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	296
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	297 # 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	298 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	299 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	300 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	301 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	302 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	303 # 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	304 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	305 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	306 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	307
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	308 # 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	309 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	310 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	311 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	312
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	313 # 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	314 out_path <- opt$outPath
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	315 dir.create(out_path, showWarnings = FALSE)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	316
14 070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	317 # Check if contrastData is a file or not
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	318 if (file.exists(opt$contrastData)) {
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	319 contrast_data <- unlist(read.table(opt$contrastData, sep = "\t", header = TRUE)[[1]])
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	320 } else {
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	321 # Split up contrasts separated by comma into a vector then sanitise
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	322 contrast_data <- unlist(strsplit(opt$contrastData, split = ","))
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	323 }
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	324 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	325 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	326
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	327 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	328 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	329 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	330 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	331 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	332 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	333 for (i 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	334 mds_pdf[i] <- make_out(paste0("mdsplot_", names(factors)[i], ".pdf"))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	335 mds_png[i] <- make_out(paste0("mdsplot_", 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	336 }
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	337 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	338 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	339 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	340 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	341 md_pdf[i] <- make_out(paste0("mdplot_", contrast_data[i], ".pdf"))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	342 md_png[i] <- make_out(paste0("mdplot_", contrast_data[i], ".png"))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	343 top_out[i] <- make_out(paste0("edgeR_", contrast_data[i], ".tsv"))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	344 } # 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	345 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	346 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	347 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	348
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	349 # 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	350 # Link
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	351 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	352 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	353
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	354 # 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	355 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	356 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	357 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	358
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 ### Data Processing
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	361 ################################################################################
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	362
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	363 # 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	364 data <- list()
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	365 data$counts <- counts
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	366 if (have_anno) {
3 d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	367 # order annotation by genes in counts (assumes gene ids are in 1st column of geneanno)
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	368 annoord <- geneanno[match(row.names(counts), geneanno[, 1]), ]
3 d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	369 data$genes <- annoord
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	370 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	371 data$genes <- data.frame(GeneID = row.names(counts))
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	372 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	373
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	374 # If filter crieteria set, filter out genes that do not have a required cpm/counts in a required number of
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	375 # samples. Default is no filtering
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	376 prefilter_count <- nrow(data$counts)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	377
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	378 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	379 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	380 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	381 } 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	382 keep <- rowSums(data$counts >= opt$cntReq) >= opt$sampleReq
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	383 } else if (filt_cpm) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	384 keep <- rowSums(cpm(data$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	385 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	386
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	387 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	388 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	389 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	390
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	391 postfilter_count <- nrow(data$counts)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	392 filtered_count <- prefilter_count - postfilter_count
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	393
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	394 # Name rows of factors according to their sample
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	395 row.names(factors) <- names(data$counts)
12 a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 9 diff changeset	396 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	397
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	398 # 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	399 samplenames <- colnames(data$counts)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	400 genes <- data$genes
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	401 data <- DGEList(data$counts)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	402 colnames(data) <- samplenames
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	403 data$samples <- factors
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	404 data$genes <- genes
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	405
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	406
14 070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	407 if (!is.null(opt$formula)) {
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	408 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	409 # 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	410 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	411 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	412 }
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	413 } else {
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	414 formula <- "~0"
070900306913 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 0c79416d9612d0ebdcb7c3c0543d510e11bb0774 iuc parents: 13 diff changeset	415 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	416 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	417 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	418 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	419
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	420 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	421 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	422
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	423 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	424 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	425 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	426
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	427 # 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	428 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	429
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	430 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	431 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	432 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	433 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	434 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	435
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	436 # 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	437 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	438
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	439 ################################################################################
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	440 ### Data Output
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
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	443 # Plot MDS
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	444 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	445
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	446 # 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	447 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	448 plotMDS(data, labels = labels, col = as.numeric(factors[, 1]), cex = 0.8, main = paste("MDS Plot:", names(factors)[1]))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	449 img_name <- paste0("MDS Plot_", names(factors)[1], ".png")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	450 img_addr <- paste0("mdsplot_", names(factors)[1], ".png")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	451 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	452 invisible(dev.off())
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	453
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	454 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	455 plotMDS(data, labels = labels, col = as.numeric(factors[, 1]), cex = 0.8, main = paste("MDS Plot:", names(factors)[1]))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	456 link_name <- paste0("MDS Plot_", names(factors)[1], ".pdf")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	457 link_addr <- paste0("mdsplot_", names(factors)[1], ".pdf")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	458 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	459 invisible(dev.off())
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	460
3 d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	461 # 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	462 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	463 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	464 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	465 plotMDS(data, labels = labels, col = as.numeric(factors[, i]), cex = 0.8, main = paste("MDS Plot:", 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	466 img_name <- paste0("MDS Plot_", names(factors)[i], ".png")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	467 img_addr <- paste0("mdsplot_", names(factors)[i], ".png")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	468 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	469 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	470
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	471 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	472 plotMDS(data, labels = labels, col = as.numeric(factors[, i]), cex = 0.8, main = paste("MDS Plot:", 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	473 link_name <- paste0("MDS Plot_", names(factors)[i], ".pdf")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	474 link_addr <- paste0("mdsplot_", names(factors)[i], ".pdf")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	475 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	476 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	477 }
3 d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	478 }
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	479
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	480 # 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	481 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	482 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	483 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	484 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	485 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	486 invisible(dev.off())
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	487
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	488 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	489 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	490 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	491 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	492 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	493 invisible(dev.off())
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	494
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	495 # 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	496 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	497 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	498 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	499 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	500 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	501 } else {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	502 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	503 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	504
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	505 # 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	506 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	507 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	508 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	509 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	510 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	511 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	512
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	513 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	514 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	515 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	516 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	517 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	518 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	519 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	520
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	521 # 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	522 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	523 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	524 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	525 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	526 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	527 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	528
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	529
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	530 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	531 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	532 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	533 } else {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	534 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	535 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	536
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	537 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	538 adjust.method = opt$pAdjOpt, p.value = opt$pValReq,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	539 lfc = opt$lfcReq
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	540 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	541 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	542
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	543 # 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	544 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	545 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	546 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	547
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	548 # 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	549 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	550 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	551
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	552 link_name <- paste0("edgeR_", contrast_data[i], ".tsv")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	553 link_addr <- paste0("edgeR_", contrast_data[i], ".tsv")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	554 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	555
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	556 # 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	557 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	558 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	559 status = status,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	560 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	561 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	562 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	563 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	564
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	565 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	566
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	567 link_name <- paste0("MD Plot_", contrast_data[i], ".pdf")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	568 link_addr <- paste0("mdplot_", contrast_data[i], ".pdf")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	569 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	570 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	571
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	572 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	573 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	574 status = status,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	575 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	576 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	577 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	578 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	579
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	580 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	581
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	582 img_name <- paste0("MD Plot_", contrast_data[i], ".png")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	583 img_addr <- paste0("mdplot_", contrast_data[i], ".png")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	584 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	585 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	586 }
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	587 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	588 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	589
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	590 # 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	591 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	592 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	593 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	594 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	595 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	596 } else {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	597 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	598 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	599 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	600 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	601 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	602 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	603
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	604 # 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	605 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	606 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	607
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	608 # 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	609 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	610 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	611 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	612
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 ### HTML Generation
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	615 ################################################################################
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	616
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	617 # 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	618 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	619
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	620 cata("<html>\n")
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 cata("<body>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	623 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	624 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	625
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	626 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	627
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	628 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	629 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	630 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	631
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	632 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	633
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	634 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	635 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	636 table_item()
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	637 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	638 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	639 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	640 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	641 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	642 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	643 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	644 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	645 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	646 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	647 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	648 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	649 cata("</table>")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	650
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	651 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	652 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	653 if (grepl(".pdf", link_data$Link[i])) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	654 html_link(link_data$Link[i], link_data$Label[i])
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	655 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	656 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	657
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	658 cata("<h4>Tables:</h4>\n")
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	659 for (i in seq_len(nrow(link_data))) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	660 if (grepl(".tsv", link_data$Link[i])) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	661 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	662 }
0 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
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	665 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	666 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	667 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	668 if (grepl(".RData", link_data$Link[i])) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	669 html_link(link_data$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	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 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	672 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	673
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	674 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	675 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	676 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	677 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	678
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	679 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	680 cata("<ul>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	681
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	682 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	683 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	684 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	685 "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	686 "CPM in at least", opt$sampleReq, "samples are insignificant",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	687 "and filtered out."
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	688 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	689 } else if (filt_smpcount) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	690 temp_str <- paste(
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	691 "Genes without more than", opt$cntReq,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	692 "counts in at least", opt$sampleReq, "samples are insignificant",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	693 "and filtered out."
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	694 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	695 } else if (filt_totcount) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	696 temp_str <- paste(
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	697 "Genes without more than", opt$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, 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	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 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	702
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	703 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	704 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	705 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	706 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	707 "%) 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	708 )
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)
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	710 }
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	711 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	712 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	713 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	714 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	715 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	716 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	717 } else {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	718 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	719 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	720 }
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 (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	722 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	723 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	724 "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	725 "of ", opt$pValReq, " and exhibit log2-fold-change of at ",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	726 "least ", opt$lfcReq, "."
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	727 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	728 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	729 } else if (opt$pAdjOpt == "holm") {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	730 temp_str <- paste0(
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	731 "MD-Plot highlighted genes are significant at adjusted ",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	732 "p-value of ", opt$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	733 "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	734 opt$lfcReq, "."
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	735 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	736 list_item(temp_str)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	737 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	738 } else {
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	739 temp_str <- paste0(
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	740 "MD-Plot highlighted genes are significant at p-value ",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	741 "of ", opt$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	742 "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	743 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	744 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	745 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	746 cata("</ul>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	747
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	748 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	749
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	750 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	751
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	752 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	753 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	754 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	755 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	756
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	757 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	758 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	759 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	760 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	761 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	762 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	763
8 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 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	765 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	766 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	767 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	768 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	769 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	770 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	771 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	772 cata("</table>")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	773
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 6 diff changeset	774 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	775 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	776 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	777 }
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	778 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	779
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	780 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	781 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	782 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	783 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	784 cata("</tr>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	785 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	786 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	787 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	788 cata("</tr>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	789 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	790 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	791 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	792 cata("<tr>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	793 cata("</table>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	794
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	795 cata("</body>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	796 cata("</html>")

Mercurial > repos > iuc > edger

annotate edger.R @ 14:070900306913 draft