nanopore_qc: nanopore

annotate nanopore_qc.R @ 10:e5a2720176d1 draft default tip

"planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 70f0b9a3a9835fd60acbb6d08efd0d5c15c97458"

author	jdv
date	Fri, 23 Aug 2019 18:16:53 -0400
parents	0cf41189f086
children

rev	line source
0 192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	1 #!/usr/bin/Rscript
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	2
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	3 # MinionQC version 1.0
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	4 # Copyright (C) 2017 Robert Lanfear
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	5 #
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	6 # This program is free software: you can redistribute it and/or modify it under
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	7 # the terms of the GNU General Public License as published by the Free Software
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	8 # Foundation, either version 3 of the License, or (at your option) any later
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	9 # version.
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	10 #
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	11 # This program is distributed in the hope that it will be useful, but WITHOUT
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	12 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	13 # FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	14 # details. You should have received a copy of the GNU General Public License
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	15 # along with this program. If not, see <http://www.gnu.org/licenses/>.
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	16
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	17
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	18 # supress warnings
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	19 options(warn=-1)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	20
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	21 library(ggplot2)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	22 library(plyr)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	23 library(reshape2)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	24 library(readr)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	25 library(yaml)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	26 suppressMessages(library(scales))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	27 #library(parallel)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	28 library(futile.logger)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	29 suppressPackageStartupMessages(library(data.table))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	30 suppressPackageStartupMessages(library(optparse))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	31
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	32
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	33 # option parsing #
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	34
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	35 parser <- OptionParser()
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	36
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	37 parser <- add_option(parser,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	38 opt_str = c("-i", "--input"),
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	39 type = "character",
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	40 dest = 'input.file',
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	41 help="Input file or directory (required). Either a full path to a sequence_summary.txt file, or a full path to a directory containing one or more such files. In the latter case the directory is searched recursively."
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	42 )
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	43
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	44 parser <- add_option(parser,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	45 opt_str = c("-o", "--outputdirectory"),
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	46 type = "character",
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	47 dest = 'output.dir',
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	48 help="Output directory (required). If a single sequencing_summary.txt file is passed as input, then the output directory will contain just the plots associated with that file. If a directory containing more than one sequencing_summary.txt files is passed as input, then the plots will be put into sub-directories that have the same names as the parent directories of each sequencing_summary.txt file"
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	49 )
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	50
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	51 parser <- add_option(parser,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	52 opt_str = c("-q", "--qscore_cutoff"),
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	53 type="double",
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	54 default=7.0,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	55 dest = 'q',
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	56 help="The cutoff value for the mean Q score of a read (default 7). Used to create separate plots for reads above and below this threshold"
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	57 )
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	58
6 0cf41189f086 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 0d8d1ec70b450f96a29a98e4dec9688b18170d32 jdv parents: 4 diff changeset	59 parser <- add_option(parser,
0cf41189f086 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 0d8d1ec70b450f96a29a98e4dec9688b18170d32 jdv parents: 4 diff changeset	60 opt_str = c("-d", "--discard_failed"),
0cf41189f086 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 0d8d1ec70b450f96a29a98e4dec9688b18170d32 jdv parents: 4 diff changeset	61 type="logical",
0cf41189f086 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 0d8d1ec70b450f96a29a98e4dec9688b18170d32 jdv parents: 4 diff changeset	62 default=FALSE,
0cf41189f086 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 0d8d1ec70b450f96a29a98e4dec9688b18170d32 jdv parents: 4 diff changeset	63 dest = 'filt.failed',
0cf41189f086 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 0d8d1ec70b450f96a29a98e4dec9688b18170d32 jdv parents: 4 diff changeset	64 help="Discard reads that failed Albacore filtering"
0cf41189f086 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 0d8d1ec70b450f96a29a98e4dec9688b18170d32 jdv parents: 4 diff changeset	65 )
0cf41189f086 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 0d8d1ec70b450f96a29a98e4dec9688b18170d32 jdv parents: 4 diff changeset	66
0 192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	67 opt = parse_args(parser)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	68
6 0cf41189f086 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 0d8d1ec70b450f96a29a98e4dec9688b18170d32 jdv parents: 4 diff changeset	69 input.file = opt$input.file
0cf41189f086 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 0d8d1ec70b450f96a29a98e4dec9688b18170d32 jdv parents: 4 diff changeset	70 output.dir = opt$output.dir
0cf41189f086 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 0d8d1ec70b450f96a29a98e4dec9688b18170d32 jdv parents: 4 diff changeset	71 filt.failed = opt$filt.failed
0cf41189f086 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 0d8d1ec70b450f96a29a98e4dec9688b18170d32 jdv parents: 4 diff changeset	72 q = opt$q
0 192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	73
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	74 # this is how we label the reads at least as good as q
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	75 q_title = paste("Q>=", q, sep="")
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	76
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	77
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	78 # build the map for R9.5
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	79 p1 = data.frame(channel=33:64, row=rep(1:4, each=8), col=rep(1:8, 4))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	80 p2 = data.frame(channel=481:512, row=rep(5:8, each=8), col=rep(1:8, 4))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	81 p3 = data.frame(channel=417:448, row=rep(9:12, each=8), col=rep(1:8, 4))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	82 p4 = data.frame(channel=353:384, row=rep(13:16, each=8), col=rep(1:8, 4))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	83 p5 = data.frame(channel=289:320, row=rep(17:20, each=8), col=rep(1:8, 4))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	84 p6 = data.frame(channel=225:256, row=rep(21:24, each=8), col=rep(1:8, 4))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	85 p7 = data.frame(channel=161:192, row=rep(25:28, each=8), col=rep(1:8, 4))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	86 p8 = data.frame(channel=97:128, row=rep(29:32, each=8), col=rep(1:8, 4))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	87
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	88 q1 = data.frame(channel=1:32, row=rep(1:4, each=8), col=rep(16:9, 4))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	89 q2 = data.frame(channel=449:480, row=rep(5:8, each=8), col=rep(16:9, 4))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	90 q3 = data.frame(channel=385:416, row=rep(9:12, each=8), col=rep(16:9, 4))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	91 q4 = data.frame(channel=321:352, row=rep(13:16, each=8), col=rep(16:9, 4))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	92 q5 = data.frame(channel=257:288, row=rep(17:20, each=8), col=rep(16:9, 4))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	93 q6 = data.frame(channel=193:224, row=rep(21:24, each=8), col=rep(16:9, 4))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	94 q7 = data.frame(channel=129:160, row=rep(25:28, each=8), col=rep(16:9, 4))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	95 q8 = data.frame(channel=65:96, row=rep(29:32, each=8), col=rep(16:9, 4))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	96
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	97 map = rbind(p1, p2, p3, p4, p5, p6, p7, p8, q1, q2, q3, q4, q5, q6, q7, q8)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	98
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	99 add_cols <- function(d, min.q){
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	100 # take a sequencing sumamry file (d), and a minimum Q value you are interested in (min.q)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	101 # return the same data frame with the following columns added
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	102 # cumulative.bases
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	103 # hour of run
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	104 # reads.per.hour
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	105
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	106 d = subset(d, mean_qscore_template >= min.q)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	107
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	108 if(nrow(d)==0){
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	109 flog.error(paste("There are no reads with a mean Q score higher than your cutoff of ", min.q, ". Please choose a lower cutoff and try again.", sep = ""))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	110 quit()
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	111 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	112
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	113 d = merge(d, map, by="channel")
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	114 d = d[with(d, order(start_time)), ] # sort by read length
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	115 d$cumulative.bases.time = cumsum(as.numeric(d$start_time))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	116 d = d[with(d, order(-sequence_length_template)), ] # sort by read length
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	117 d$cumulative.bases = cumsum(as.numeric(d$sequence_length_template))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	118 d$hour = d$start_time %/% 3600
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	119
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	120 # add the reads generated for each hour
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	121 reads.per.hour = as.data.frame(table(d$hour))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	122 names(reads.per.hour) = c("hour", "reads_per_hour")
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	123 reads.per.hour$hour = as.numeric(as.character(reads.per.hour$hour))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	124 d = merge(d, reads.per.hour, by = c("hour"))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	125 return(d)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	126 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	127
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	128
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	129 load_summary <- function(filepath, min.q){
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	130 # load a sequencing summary and add some info
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	131 # min.q is a vector of length 2 defining 2 levels of min.q to have
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	132 # by default the lowest value is -Inf, i.e. includes all reads. The
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	133 # other value in min.q is set by the user at the command line
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	134 d = read_tsv(filepath, col_types = cols_only(channel = 'i',
6 0cf41189f086 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 0d8d1ec70b450f96a29a98e4dec9688b18170d32 jdv parents: 4 diff changeset	135 passes_filtering = 'c',
0 192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	136 num_events_template = 'i',
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	137 sequence_length_template = 'i',
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	138 mean_qscore_template = 'n',
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	139 sequence_length_2d = 'i',
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	140 mean_qscore_2d = 'n',
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	141 start_time = 'n'))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	142
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	143 if("sequence_length_2d" %in% names(d)){
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	144 # it's a 1D2 or 2D run
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	145 d$sequence_length_template = as.numeric(as.character(d$sequence_length_2d))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	146 d$mean_qscore_template = as.numeric(as.character(d$mean_qscore_2d))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	147 d$num_events_template = NA
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	148 d$start_time = as.numeric(as.character(d$start_time))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	149
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	150 }else{
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	151 d$sequence_length_template = as.numeric(as.character(d$sequence_length_template))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	152 d$mean_qscore_template = as.numeric(as.character(d$mean_qscore_template))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	153 d$num_events_template = as.numeric(as.character(d$num_events_template))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	154 d$start_time = as.numeric(as.character(d$start_time))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	155 }
4 4b7d1bcf210c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit dfa6f9934da27ffddc4da6c16d97d4057662ef65 jdv parents: 0 diff changeset	156
4b7d1bcf210c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit dfa6f9934da27ffddc4da6c16d97d4057662ef65 jdv parents: 0 diff changeset	157 # ignore 0-length reads
4b7d1bcf210c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit dfa6f9934da27ffddc4da6c16d97d4057662ef65 jdv parents: 0 diff changeset	158 d <- d[d$sequence_length_template > 0,]
6 0cf41189f086 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 0d8d1ec70b450f96a29a98e4dec9688b18170d32 jdv parents: 4 diff changeset	159 # ignore reads failing filtering
0cf41189f086 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 0d8d1ec70b450f96a29a98e4dec9688b18170d32 jdv parents: 4 diff changeset	160 if (filt.failed) {
0cf41189f086 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 0d8d1ec70b450f96a29a98e4dec9688b18170d32 jdv parents: 4 diff changeset	161 d <- d[d$passes_filtering == 'True',]
0cf41189f086 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 0d8d1ec70b450f96a29a98e4dec9688b18170d32 jdv parents: 4 diff changeset	162 }
0 192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	163
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	164 d$events_per_base = d$num_events_template/d$sequence_length_template
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	165
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	166 flowcell = basename(dirname(filepath))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	167
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	168 # add columns for all the reads
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	169 d1 = add_cols(d, min.q[1])
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	170 d1$Q_cutoff = "All reads"
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	171
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	172 # add columns for just the reads that pass the user Q threshold
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	173 d2 = add_cols(d, min.q[2])
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	174 d2$Q_cutoff = q_title
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	175
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	176 # bind those two together into one data frame
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	177 d = as.data.frame(rbindlist(list(d1, d2)))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	178
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	179 # name the flowcell (useful for analyses with >1 flowcell)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	180 d$flowcell = flowcell
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	181
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	182 # make sure this is a factor
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	183 d$Q_cutoff = as.factor(d$Q_cutoff)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	184
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	185
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	186 keep = c("hour","start_time", "channel", "sequence_length_template", "mean_qscore_template", "row", "col", "cumulative.bases", "cumulative.bases.time", "reads_per_hour", "Q_cutoff", "flowcell", "events_per_base")
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	187 d = d[keep]
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	188
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	189 d$start_bin = cut(d$start_time, 9,labels=c(1:9))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	190
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	191 return(d)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	192 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	193
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	194 reads.gt <- function(d, len){
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	195 # return the number of reads in data frame d
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	196 # that are at least as long as length len
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	197 return(length(which(d$sequence_length_template>=len)))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	198 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	199
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	200 bases.gt <- function(d, len){
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	201 # return the number of bases contained in reads from
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	202 # data frame d
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	203 # that are at least as long as length len
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	204 reads = subset(d, sequence_length_template >= len)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	205 return(sum(as.numeric(reads$sequence_length_template)))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	206 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	207
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	208 log10_minor_break = function (...){
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	209 # function to add minor breaks to a log10 graph
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	210 # hat-tip: https://stackoverflow.com/questions/30179442/plotting-minor-breaks-on-a-log-scale-with-ggplot
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	211 function(x) {
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	212 minx = floor(min(log10(x), na.rm=T))-1;
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	213 maxx = ceiling(max(log10(x), na.rm=T))+1;
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	214 n_major = maxx-minx+1;
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	215 major_breaks = seq(minx, maxx, by=1)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	216 minor_breaks =
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	217 rep(log10(seq(1, 9, by=1)), times = n_major)+
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	218 rep(major_breaks, each = 9)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	219 return(10^(minor_breaks))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	220 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	221 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	222
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	223 binSearch <- function(min, max, df, t = 100000) {
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	224 # binary search algorithm, thanks to https://stackoverflow.com/questions/46292438/optimising-a-calculation-on-every-cumulative-subset-of-a-vector-in-r/46303384#46303384
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	225 # the aim is to return the number of reads in a dataset (df)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	226 # that comprise the largest subset of reads with an N50 of t
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	227 # we use this to calculte the number of 'ultra long' reads
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	228 # which are defined as those with N50 > 100KB
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	229 mid = floor(mean(c(min, max)))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	230 if (mid == min) {
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	231 if (df$sequence_length_template[min(which(df$cumulative.bases>df$cumulative.bases[min]/2))] < t) {
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	232 return(min - 1)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	233 } else {
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	234 return(max - 1)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	235 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	236 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	237
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	238 n = df$sequence_length_template[min(which(df$cumulative.bases>df$cumulative.bases[mid]/2))]
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	239 if (n >= t) {
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	240 return(binSearch(mid, max, df))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	241 } else {
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	242 return(binSearch(min, mid, df))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	243 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	244 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	245
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	246
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	247 summary.stats <- function(d, Q_cutoff="All reads"){
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	248 # Calculate summary stats for a single value of min.q
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	249
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	250 rows = which(as.character(d$Q_cutoff)==Q_cutoff)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	251 d = d[rows,]
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	252 d = d[with(d, order(-sequence_length_template)), ] # sort by read length, just in case
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	253
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	254 total.bases = sum(as.numeric(d$sequence_length_template))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	255 total.reads = nrow(d)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	256 N50.length = d$sequence_length_template[min(which(d$cumulative.bases > (total.bases/2)))]
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	257 mean.length = round(mean(as.numeric(d$sequence_length_template)), digits = 1)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	258 median.length = round(median(as.numeric(d$sequence_length_template)), digits = 1)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	259 max.length = max(as.numeric(d$sequence_length_template))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	260 mean.q = round(mean(d$mean_qscore_template), digits = 1)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	261 median.q = round(median(d$mean_qscore_template), digits = 1)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	262
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	263 #calculate ultra-long reads and bases (max amount of data with N50>100KB)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	264 ultra.reads = binSearch(1, nrow(d), d, t = 100000)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	265 if(ultra.reads>=1){
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	266 ultra.gigabases = sum(as.numeric(d$sequence_length_template[1:ultra.reads]))/1000000000
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	267 }else{
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	268 ultra.gigabases = 0
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	269 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	270
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	271 reads = list(
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	272 reads.gt(d, 10000),
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	273 reads.gt(d, 20000),
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	274 reads.gt(d, 50000),
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	275 reads.gt(d, 100000),
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	276 reads.gt(d, 200000),
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	277 reads.gt(d, 500000),
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	278 reads.gt(d, 1000000),
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	279 ultra.reads)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	280 names(reads) = c(">10kb", ">20kb", ">50kb", ">100kb", ">200kb", ">500kb", ">1m", "ultralong")
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	281
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	282 bases = list(
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	283 bases.gt(d, 10000)/1000000000,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	284 bases.gt(d, 20000)/1000000000,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	285 bases.gt(d, 50000)/1000000000,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	286 bases.gt(d, 100000)/1000000000,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	287 bases.gt(d, 200000)/1000000000,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	288 bases.gt(d, 500000)/1000000000,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	289 bases.gt(d, 1000000)/1000000000,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	290 ultra.gigabases)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	291 names(bases) = c(">10kb", ">20kb", ">50kb", ">100kb", ">200kb", ">500kb", ">1m", "ultralong")
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	292
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	293 return(list('total.gigabases' = total.bases/1000000000,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	294 'total.reads' = total.reads,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	295 'N50.length' = N50.length,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	296 'mean.length' = mean.length,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	297 'median.length' = median.length,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	298 'max.length' = max.length,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	299 'mean.q' = mean.q,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	300 'median.q' = median.q,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	301 'reads' = reads,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	302 'gigabases' = bases
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	303 ))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	304 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	305
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	306 channel.summary <- function(d){
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	307 # calculate summaries of what happened in each of the channels
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	308 # of a flowcell
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	309
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	310 a = ddply(d, .(channel),
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	311 summarize,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	312 total.bases = sum(sequence_length_template),
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	313 total.reads = sum(which(sequence_length_template>=0)),
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	314 mean.read.length = mean(sequence_length_template),
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	315 median.read.length = median(sequence_length_template))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	316 b = melt(a, id.vars = c("channel"))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	317 return(b)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	318 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	319
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	320
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	321 single.flowcell <- function(input.file, output.dir, q=8){
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	322 # wrapper function to analyse data from a single flowcell
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	323 # input.file is a sequencing_summary.txt file from a 1D run
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	324 # output.dir is the output directory into which to write results
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	325 # q is the cutoff used for Q values, set by the user
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	326 flog.info(paste("Loading input file:", input.file))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	327 d = load_summary(input.file, min.q=c(-Inf, q))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	328
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	329 flowcell = unique(d$flowcell)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	330
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	331 flog.info(paste(sep = "", flowcell, ": creating output directory:", output.dir))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	332 dir.create(output.dir)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	333 out.txt = file.path(output.dir, "summary.yaml")
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	334
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	335 flog.info(paste(sep = "", flowcell, ": summarising input file for flowcell"))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	336 all.reads.summary = summary.stats(d, Q_cutoff = "All reads")
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	337 q10.reads.summary = summary.stats(d, Q_cutoff = q_title)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	338
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	339 summary = list("input file" = input.file,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	340 "All reads" = all.reads.summary,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	341 cutoff = q10.reads.summary,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	342 "notes" = 'ultralong reads refers to the largest set of reads with N50>100KB')
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	343
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	344 names(summary)[3] = q_title
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	345
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	346 write(as.yaml(summary), out.txt)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	347
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	348 muxes = seq(from = 0, to = max(d$hour), by = 8)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	349
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	350 # make plots
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	351 flog.info(paste(sep = "", flowcell, ": plotting length histogram"))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	352 len.lims <- quantile(d$sequence_length_template,c(0.01,0.99))
4 4b7d1bcf210c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit dfa6f9934da27ffddc4da6c16d97d4057662ef65 jdv parents: 0 diff changeset	353 len.lims[1] <- max(1,len.lims[1])
0 192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	354
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	355 p1 = ggplot(d, aes(x = sequence_length_template)) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	356 geom_histogram(bins = 200, fill="steelblue") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	357 scale_x_log10(breaks=round(10^pretty(log10(len.lims),n=5),0),limits=len.lims) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	358 facet_wrap(~Q_cutoff, ncol = 1, scales = "free_y") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	359 #theme(text = element_text(size = 15)) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	360 theme_linedraw() +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	361 xlab("Read length") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	362 ylab("Number of reads")
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	363 ggsave(filename = file.path(output.dir, "length_histogram.png"), width = 7, height = 4, dpi=300, plot = p1)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	364 ggsave(filename = file.path(output.dir, "length_histogram.screen.png"), width = 7, height = 4, dpi=90, plot = p1)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	365
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	366 flog.info(paste(sep = "", flowcell, ": plotting mean Q score histogram"))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	367 q.lims <- quantile(d$mean_qscore_template,c(0.005,0.995))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	368 p2 = ggplot(subset(d, Q_cutoff=="All reads"), aes(x = mean_qscore_template)) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	369 geom_histogram(bins = 200, fill="steelblue") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	370 xlim(q.lims) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	371 geom_vline(xintercept=q) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	372 #theme(text = element_text(size = 15)) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	373 theme_linedraw() +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	374 xlab("Mean Q score of read") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	375 ylab("Number of reads")
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	376 ggsave(filename = file.path(output.dir, "q_histogram.png"), width = 7, height = 4, dpi=300, plot = p2)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	377 ggsave(filename = file.path(output.dir, "q_histogram.screen.png"), width = 7, height = 4, dpi=90, plot = p2)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	378
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	379
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	380 flog.info(paste(sep = "", flowcell, ": plotting flowcell overview"))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	381
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	382 df <- data.frame(row=integer(),col=integer(),bin=integer(), quality=numeric())
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	383
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	384 # swap rows and columns
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	385 for (b in c(1,5,9)) {
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	386 m <- matrix(data=rep(0,512),nrow=16,ncol=32)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	387 for (r in 1:32) {
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	388 for (c in 1:16) {
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	389 sub <- subset(d, Q_cutoff=="All reads" & col == c & row == r & start_bin == b)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	390 Q <- median(sub$mean_qscore_template)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	391 df <- rbind(df, list(row=r, col=c, bin=b, quality=Q) )
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	392 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	393 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	394 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	395
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	396 df$bin <- factor(df$bin)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	397 levels(df$bin) <- c("Run start", "Run middle", "Run end")
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	398 p5 = ggplot(df, aes(col, row)) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	399 geom_tile(aes(fill = quality), color="white") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	400 scale_fill_gradient(low = "white", high="steelblue") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	401 xlab("Column") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	402 ylab("Row") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	403 facet_wrap(~bin, ncol=3) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	404 theme_linedraw() +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	405 theme(panel.grid.minor = element_blank(), panel.grid.major=element_blank())
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	406 #theme(text = element_text(size = 40), axis.text.x = element_text(size=12), axis.text.y = element_text(size=12), legend.text=element_text(size=12))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	407 ggsave(filename = file.path(output.dir, "flowcell_overview.png"), width = 7, height = 4, dpi=300, plot = p5)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	408 ggsave(filename = file.path(output.dir, "flowcell_overview.screen.png"), width = 7, height = 4, dpi=90, plot = p5)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	409
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	410 flog.info(paste(sep = "", flowcell, ": plotting cumulative yield summary"))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	411 p5a = ggplot(d, aes(x=start_time/3600, y=cumulative.bases.time, colour = Q_cutoff)) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	412 geom_line(size = 1) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	413 geom_vline(xintercept = muxes, colour = 'red', linetype = 'dashed', alpha = 0.5) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	414 xlab("Elapsed time (hrs)") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	415 ylab("Total yield in bases") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	416 scale_colour_discrete(guide = guide_legend(title = "Reads")) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	417 scale_x_continuous() +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	418 theme_linedraw()
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	419 #theme(text = element_text(size = 15))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	420
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	421 ggsave(filename = file.path(output.dir, "cumulative_yield.png"), width = 7, height = 4, dpi=300, plot = p5a)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	422 ggsave(filename = file.path(output.dir, "cumulative_yield.screen.png"), width = 7, height = 4, dpi=90, plot = p5a)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	423
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	424 flog.info(paste(sep = "", flowcell, ": plotting flowcell yield summary"))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	425 p6 = ggplot(d, aes(x=sequence_length_template, y=cumulative.bases, colour = Q_cutoff)) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	426 geom_line(size = 1) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	427 xlab("Minimum read length") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	428 ylab("Total yield in bases") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	429 scale_colour_discrete(guide = guide_legend(title = "Reads")) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	430 #theme(text = element_text(size = 15))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	431 theme_linedraw()
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	432 xmax = max(d$sequence_length_template[which(d$cumulative.bases > 0.01 * max(d$cumulative.bases))])
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	433 p6 = p6 + scale_x_continuous(limits = c(0, xmax))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	434
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	435 ggsave(filename = file.path(output.dir, "yield_summary.png"), width = 7, height = 4, dpi=300, plot = p6)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	436 ggsave(filename = file.path(output.dir, "yield_summary.screen.png"), width = 7, height = 4, dpi=90, plot = p6)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	437
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	438 flog.info(paste(sep = "", flowcell, ": plotting sequence length over time"))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	439 e = subset(d, Q_cutoff=="All reads")
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	440 e$Q = paste(">=", q, sep="")
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	441 e$Q[which(e$mean_qscore_template<q)] = paste("<", q, sep="")
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	442 p7 = ggplot(e, aes(x=start_time/3600, y=sequence_length_template, colour = Q, group = Q)) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	443 geom_vline(xintercept = muxes, colour = 'red', linetype = 'dashed', alpha = 0.5) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	444 geom_smooth() +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	445 xlab("Elapsed time (hrs)") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	446 ylab("Mean read length") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	447 ylim(0, NA) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	448 theme_linedraw()
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	449 ggsave(filename = file.path(output.dir, "length_by_hour.png"), width = 7, height = 4, dpi=300, plot = p7)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	450 ggsave(filename = file.path(output.dir, "length_by_hour.screen.png"), width = 7, height = 4, dpi=90, plot = p7)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	451
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	452 flog.info(paste(sep = "", flowcell, ": plotting Q score over time"))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	453 p8 = ggplot(e, aes(x=start_time/3600, y=mean_qscore_template, colour = Q, group = Q)) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	454 geom_vline(xintercept = muxes, colour = 'red', linetype = 'dashed', alpha = 0.5) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	455 geom_smooth() +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	456 xlab("Elapsed time (hrs)") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	457 ylab("Mean Q score") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	458 ylim(0, NA) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	459 theme_linedraw()
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	460 ggsave(filename = file.path(output.dir, "q_by_hour.png"), width = 7, height = 4, dpi=300, plot = p8)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	461 ggsave(filename = file.path(output.dir, "q_by_hour.screen.png"), width = 7, height = 4, dpi=90, plot = p8)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	462
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	463 flog.info(paste(sep = "", flowcell, ": plotting reads per hour"))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	464 f = d[c("hour", "reads_per_hour", "Q_cutoff")]
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	465 f = f[!duplicated(f),]
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	466 g = subset(f, Q_cutoff=="All reads")
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	467 h = subset(f, Q_cutoff==q_title)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	468 max = max(f$hour)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	469 # all of this is just to fill in hours with no reads recorded
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	470 all = 0:max
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	471 add.g = all[which(all %in% g$hour == FALSE)]
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	472 if(length(add.g)>0){
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	473 add.g = data.frame(hour = add.g, reads_per_hour = 0, Q_cutoff = "All reads")
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	474 g = rbind(g, add.g)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	475 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	476 add.h = all[which(all %in% h$hour == FALSE)]
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	477 if(length(add.h)>0){
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	478 add.h = data.frame(hour = add.h, reads_per_hour = 0, Q_cutoff = q_title)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	479 h = rbind(h, add.h)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	480 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	481 i = rbind(g, h)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	482 i$Q_cutoff = as.character(i$Q_cutoff)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	483 i$Q_cutoff[which(i$Q_cutoff==q_title)] = paste("Q>=", q, sep="")
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	484 p9 = ggplot(i, aes(x=hour, y=reads_per_hour, colour = Q_cutoff, group = Q_cutoff)) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	485 geom_vline(xintercept = muxes, colour = 'red', linetype = 'dashed', alpha = 0.5) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	486 #geom_point() +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	487 geom_line(size=1) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	488 xlab("Elapsed time (hrs)") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	489 ylab("Number of reads per hour") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	490 ylim(0, NA) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	491 scale_color_discrete(guide = guide_legend(title = "Reads")) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	492 theme_linedraw()
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	493 ggsave(filename = file.path(output.dir, "reads_per_hour.png"), width = 7, height = 4, dpi=300, plot = p9)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	494 ggsave(filename = file.path(output.dir, "reads_per_hour.screen.png"), width = 7, height = 4, dpi=90, plot = p9)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	495
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	496 flog.info(paste(sep = "", flowcell, ": plotting read length vs. q score scatterplot"))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	497 p10 = ggplot(subset(d, Q_cutoff=="All reads"), aes(x = sequence_length_template, y = mean_qscore_template, colour = events_per_base)) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	498 geom_point(alpha=0.05, size = 0.4) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	499 scale_x_log10(minor_breaks=log10_minor_break()) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	500 labs(colour='Events per base\n(log scale)\n') +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	501 theme(text = element_text(size = 15)) +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	502 xlab("Read length") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	503 ylab("Mean Q score of read") +
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	504 theme_linedraw()
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	505
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	506 if(max(d$events_per_base, na.rm=T)>0){
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	507 # a catch for 1D2 runs which don't have events per base
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	508 p10 = p10 + scale_colour_distiller(trans = "log", labels = scientific, palette = 'Spectral')
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	509 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	510
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	511 ggsave(filename = file.path(output.dir, "length_vs_q.png"), width = 7, height = 4, dpi=300, plot = p10)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	512 ggsave(filename = file.path(output.dir, "length_vs_q.screen.png"), width = 7, height = 4, dpi=90, plot = p10)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	513
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	514 return(d)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	515 }
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	516
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	517 if(file_test("-f", input.file)==TRUE){
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	518 # if it's an existing file (not a folder) just run one analysis
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	519 d = single.flowcell(input.file, output.dir, q)
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	520 }else{
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	521 #WTF
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	522 flog.warn(paste("Could find a sequencing summary file in your input which was: ",
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	523 input.file,
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	524 "\nThe input must be a sequencing_summary.txt file produced by Albacore"))
192df6f6a41e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit 59d1272f707bdd73a3f7d085f96789e649d54240-dirty jdv parents: diff changeset	525 }

Mercurial > repos > jdv > nanopore_qc

annotate nanopore_qc.R @ 10:e5a2720176d1 draft default tip