mutational_patterns: mutational

annotate mutational_patterns.R @ 26:af5c65ad5317 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bc7fab3050541155f0c3e15b7f448a1802155670

author	artbio
date	Tue, 12 Jul 2022 17:44:09 +0000
parents	b00fef2b1c2c
children	9a33a5a90a2c

rev	line source
0 924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	1 # load packages that are provided in the conda env
24 ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d artbio parents: 23 diff changeset	2 options(show.error.messages = FALSE,
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	3 error = function() {
24 ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d artbio parents: 23 diff changeset	4 cat(geterrmessage(), file = stderr())
ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d artbio parents: 23 diff changeset	5 q("no", 1, FALSE)
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	6 }
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	7 )
0 924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	8 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	9 warnings()
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	10 library(optparse)
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	11 library(rjson)
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	12 library(grid)
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	13 library(gridExtra)
4 7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c" artbio parents: 3 diff changeset	14 library(scales)
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c" artbio parents: 3 diff changeset	15 library(RColorBrewer)
0 924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	16
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	17 # Arguments
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	18 option_list <- list(
0 924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	19 make_option(
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	20 "--inputs",
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	21 default = NA,
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	22 type = "character",
0 924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	23 help = "json formatted dictionary of datasets and their paths"
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	24 ),
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	25 make_option(
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	26 "--genome",
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	27 default = NA,
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	28 type = "character",
0 924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	29 help = "genome name in the BSgenome bioconductor package"
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	30 ),
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	31 make_option(
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	32 "--levels",
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	33 default = NA,
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	34 type = "character",
0 924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	35 help = "path to the tab separated file describing the levels in function of datasets"
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	36 ),
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	37 make_option(
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	38 "--cosmic_version",
18 8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	39 default = NA,
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	40 type = "character",
18 8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	41 help = "Version of the Cosmic Signature set to be used to express mutational profiles"
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	42 ),
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	43 make_option(
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	44 "--own_signatures",
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	45 default = NA,
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	46 type = "character",
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	47 help = "Path to the user-defined signature matrix"
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	48 ),
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	49 make_option(
0 924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	50 "--signum",
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	51 default = 2,
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	52 type = "integer",
18 8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	53 help = "selects the N most significant signatures in samples to express mutational profiles"
0 924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	54 ),
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	55 make_option(
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	56 "--nrun",
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	57 default = 2,
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	58 type = "integer",
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	59 help = "Number of runs to fit signatures"
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	60 ),
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	61 make_option(
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	62 "--rank",
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	63 default = 2,
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	64 type = "integer",
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	65 help = "number of ranks to display for parameter optimization"
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	66 ),
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	67 make_option(
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	68 "--newsignum",
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	69 default = 2,
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	70 type = "integer",
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	71 help = "Number of new signatures to be captured"
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	72 ),
25 b00fef2b1c2c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit eeb46055822c6805c209af0c450ae941100960bd artbio parents: 24 diff changeset	73 make_option(
b00fef2b1c2c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit eeb46055822c6805c209af0c450ae941100960bd artbio parents: 24 diff changeset	74 "--cosmic_id_threshold",
b00fef2b1c2c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit eeb46055822c6805c209af0c450ae941100960bd artbio parents: 24 diff changeset	75 default = 0.85,
b00fef2b1c2c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit eeb46055822c6805c209af0c450ae941100960bd artbio parents: 24 diff changeset	76 type = "double",
b00fef2b1c2c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit eeb46055822c6805c209af0c450ae941100960bd artbio parents: 24 diff changeset	77 help = "minimu cosine similarity to rename a new signature according to cosmic v3.2"
b00fef2b1c2c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit eeb46055822c6805c209af0c450ae941100960bd artbio parents: 24 diff changeset	78 ),
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	79 make_option(
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	80 "--output_spectrum",
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	81 default = NA,
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	82 type = "character",
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	83 help = "path to output dataset"
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	84 ),
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	85 make_option(
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	86 "--output_denovo",
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	87 default = NA,
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	88 type = "character",
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	89 help = "path to output dataset"
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	90 ),
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	91 make_option(
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	92 "--sigmatrix",
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	93 default = NA,
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	94 type = "character",
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	95 help = "path to signature matrix"
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	96 ),
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	97 make_option(
18 8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	98 "--output_sigpattern",
0 924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	99 default = NA,
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	100 type = "character",
0 924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	101 help = "path to output dataset"
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	102 ),
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	103 make_option(
23 83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	104 "--display_signatures",
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	105 default = NA,
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	106 type = "character",
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	107 help = "display input signature profiles if set to yes"
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	108 ),
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	109 make_option(
11 7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460" artbio parents: 10 diff changeset	110 "--sig_contrib_matrix",
7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460" artbio parents: 10 diff changeset	111 default = NA,
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	112 type = "character",
11 7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460" artbio parents: 10 diff changeset	113 help = "path to signature contribution matrix"
7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460" artbio parents: 10 diff changeset	114 ),
7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460" artbio parents: 10 diff changeset	115 make_option(
20 a2cb7dc9250a "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit b07cf2662a36d88f80dc08ef4f46454dbc133094" artbio parents: 19 diff changeset	116 "--colors",
a2cb7dc9250a "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit b07cf2662a36d88f80dc08ef4f46454dbc133094" artbio parents: 19 diff changeset	117 default = NA,
a2cb7dc9250a "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit b07cf2662a36d88f80dc08ef4f46454dbc133094" artbio parents: 19 diff changeset	118 type = "character",
a2cb7dc9250a "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit b07cf2662a36d88f80dc08ef4f46454dbc133094" artbio parents: 19 diff changeset	119 help = "color palette to display signatures"
a2cb7dc9250a "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit b07cf2662a36d88f80dc08ef4f46454dbc133094" artbio parents: 19 diff changeset	120 ),
a2cb7dc9250a "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit b07cf2662a36d88f80dc08ef4f46454dbc133094" artbio parents: 19 diff changeset	121 make_option(
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	122 c("-r", "--rdata"),
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	123 type = "character",
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	124 default = NULL,
17 8c6ee1c2248f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e5d498dfc5a6a9aaea3d09037dea5d15c2d85dd2" artbio parents: 16 diff changeset	125 help = "Path to RData output file"
8c6ee1c2248f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e5d498dfc5a6a9aaea3d09037dea5d15c2d85dd2" artbio parents: 16 diff changeset	126 ),
8c6ee1c2248f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e5d498dfc5a6a9aaea3d09037dea5d15c2d85dd2" artbio parents: 16 diff changeset	127 make_option(
8c6ee1c2248f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e5d498dfc5a6a9aaea3d09037dea5d15c2d85dd2" artbio parents: 16 diff changeset	128 c("-t", "--tooldir"),
8c6ee1c2248f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e5d498dfc5a6a9aaea3d09037dea5d15c2d85dd2" artbio parents: 16 diff changeset	129 type = "character",
8c6ee1c2248f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e5d498dfc5a6a9aaea3d09037dea5d15c2d85dd2" artbio parents: 16 diff changeset	130 default = NULL,
8c6ee1c2248f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e5d498dfc5a6a9aaea3d09037dea5d15c2d85dd2" artbio parents: 16 diff changeset	131 help = "Path to tool directory, where tool data are stored")
8c6ee1c2248f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e5d498dfc5a6a9aaea3d09037dea5d15c2d85dd2" artbio parents: 16 diff changeset	132
0 924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	133 )
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	134
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	135 opt <- parse_args(OptionParser(option_list = option_list),
0 924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	136 args = commandArgs(trailingOnly = TRUE))
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	137
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	138 ################ Manage input data ####################
0 924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	139 json_dict <- opt$inputs
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	140 parser <- newJSONParser()
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	141 parser$addData(json_dict)
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	142 fileslist <- parser$getObject()
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	143 vcf_paths <- attr(fileslist, "names")
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	144 element_identifiers <- unname(unlist(fileslist))
0 924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	145 ref_genome <- opt$genome
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	146 vcf_table <- data.frame(element_identifier = as.character(element_identifiers), path = vcf_paths)
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	147
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	148 library(MutationalPatterns)
0 924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	149 library(ref_genome, character.only = TRUE)
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	150 library(ggplot2)
0 924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	151
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	152 # Load the VCF files into a GRangesList:
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	153 vcfs <- read_vcfs_as_granges(vcf_paths, element_identifiers, ref_genome)
8 e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	154 library(plyr)
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	155 if (!is.na(opt$levels)[1]) { # manage levels if there are
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	156 levels_table <- read.delim(opt$levels, header = FALSE,
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	157 col.names = c("element_identifier", "level"))
8 e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	158 } else {
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	159 levels_table <- data.frame(element_identifier = vcf_table$element_identifier,
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	160 level = rep("nolabels", length(vcf_table$element_identifier)))
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	161 }
8 e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	162 metadata_table <- join(vcf_table, levels_table, by = "element_identifier")
e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	163 tissue <- as.vector(metadata_table$level)
e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	164 detach(package:plyr)
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	165
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	166 ##### This is done for any section ######
0 924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	167 mut_mat <- mut_matrix(vcf_list = vcfs, ref_genome = ref_genome)
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	168 qual_col_pals <- brewer.pal.info[brewer.pal.info$category == "qual", ]
0 924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540" artbio parents: diff changeset	169
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	170 ###### Section 1 Mutation characteristics and spectrums #############
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	171 if (!is.na(opt$output_spectrum)[1]) {
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	172 pdf(opt$output_spectrum, paper = "special", width = 11.69, height = 11.69)
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	173 type_occurrences <- mut_type_occurrences(vcfs, ref_genome)
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	174
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	175 # mutation spectrum, total or by sample
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	176
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	177 if (length(levels(factor(levels_table$level))) == 1) {
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	178 p1 <- plot_spectrum(type_occurrences, CT = TRUE, legend = TRUE)
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	179 plot(p1)
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	180 } else {
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	181 p2 <- plot_spectrum(type_occurrences, by = tissue, CT = TRUE) # by levels
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	182 p3 <- plot_spectrum(type_occurrences, CT = TRUE, legend = TRUE) # total
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	183 grid.arrange(p2, p3, ncol = 2, widths = c(4, 2.3), heights = c(4, 1))
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	184 }
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	185 plot_96_profile(mut_mat, condensed = TRUE)
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	186 dev.off()
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	187 }
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	188
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	189 ###### Section 2: De novo mutational signature extraction using NMF #######
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	190 # opt$rank cannot be higher than the number of samples and
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	191 # likewise, opt$signum cannot be higher thant the number of samples
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	192 if (!is.na(opt$output_denovo)[1]) {
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	193
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	194 if (opt$rank > length(element_identifiers)) {
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	195 opt$rank <- length(element_identifiers)
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	196 }
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	197 if (opt$signum > length(element_identifiers)) {
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	198 opt$signum <- length(element_identifiers)
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	199 }
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	200 pseudo_mut_mat <- mut_mat + 0.0001 # First add a small pseudocount to the mutation count matrix
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	201 # Use the NMF package to generate an estimate rank plot
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	202 library("NMF")
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	203 estimate <- nmf(pseudo_mut_mat, rank = 1:opt$rank, method = "brunet", nrun = opt$nrun, seed = 123456)
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	204 # And plot it
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	205 pdf(opt$output_denovo, paper = "special", width = 11.69, height = 11.69)
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	206 p4 <- plot(estimate)
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	207 grid.arrange(p4)
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	208 # Extract 4 (PARAMETIZE) mutational signatures from the mutation count matrix with extract_signatures
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	209 # (For larger datasets it is wise to perform more iterations by changing the nrun parameter
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	210 # to achieve stability and avoid local minima)
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	211 nmf_res <- extract_signatures(pseudo_mut_mat, rank = opt$newsignum, nrun = opt$nrun)
24 ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d artbio parents: 23 diff changeset	212 # Assign signature COSMICv3.2 names
ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d artbio parents: 23 diff changeset	213 cosmic_signatures <- get_known_signatures()
25 b00fef2b1c2c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit eeb46055822c6805c209af0c450ae941100960bd artbio parents: 24 diff changeset	214 nmf_res <- rename_nmf_signatures(nmf_res, cosmic_signatures, cutoff = opt$cosmic_id_threshold)
24 ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d artbio parents: 23 diff changeset	215 sim_matrix <- cos_sim_matrix(cosmic_signatures, nmf_res$signatures)
ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d artbio parents: 23 diff changeset	216 plot_cosine_sim <- plot_cosine_heatmap(sim_matrix)
ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d artbio parents: 23 diff changeset	217 grid.arrange(plot_cosine_sim)
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	218 # Plot the 96-profile of the signatures:
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	219 p5 <- plot_96_profile(nmf_res$signatures, condensed = TRUE)
25 b00fef2b1c2c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit eeb46055822c6805c209af0c450ae941100960bd artbio parents: 24 diff changeset	220 grid.arrange(p5)
b00fef2b1c2c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit eeb46055822c6805c209af0c450ae941100960bd artbio parents: 24 diff changeset	221 # write matrix of deno signatures for user
15 8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37" artbio parents: 14 diff changeset	222 new_sig_matrix <- reshape2::dcast(p5$data, substitution + context ~ sample, value.var = "freq")
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	223 new_sig_matrix <- format(new_sig_matrix, scientific = TRUE)
24 ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d artbio parents: 23 diff changeset	224 newcol <- paste0(gsub("\\..", "", new_sig_matrix$context, perl = TRUE),
23 83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	225 "[", new_sig_matrix$substitution, "]",
24 ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d artbio parents: 23 diff changeset	226 gsub("^.\\.", "", new_sig_matrix$context, perl = TRUE))
23 83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	227 new_sig_matrix <- cbind(Type = newcol, new_sig_matrix[, seq_along(new_sig_matrix)[-c(1, 2)]])
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	228 write.table(new_sig_matrix, file = opt$sigmatrix, quote = FALSE, row.names = FALSE, sep = "\t")
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	229 # Visualize the contribution of the signatures in a barplot
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	230 pc1 <- plot_contribution(nmf_res$contribution, nmf_res$signature, mode = "relative", coord_flip = TRUE)
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	231 # Visualize the contribution of the signatures in absolute number of mutations
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	232 pc2 <- plot_contribution(nmf_res$contribution, nmf_res$signature, mode = "absolute", coord_flip = TRUE)
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	233 # Combine the two plots:
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	234 grid.arrange(pc1, pc2)
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	235
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	236 # The relative contribution of each signature for each sample can also be plotted as a heatmap with
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	237 # plot_contribution_heatmap, which might be easier to interpret and compare than stacked barplots.
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	238 # The samples can be hierarchically clustered based on their euclidean dis- tance. The signatures
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	239 # can be plotted in a user-specified order.
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	240 # Plot signature contribution as a heatmap with sample clustering dendrogram and a specified signature order:
25 b00fef2b1c2c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit eeb46055822c6805c209af0c450ae941100960bd artbio parents: 24 diff changeset	241 pch1 <- plot_contribution_heatmap(nmf_res$contribution, cluster_samples = TRUE)
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	242 # Plot signature contribution as a heatmap without sample clustering:
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	243 pch2 <- plot_contribution_heatmap(nmf_res$contribution, cluster_samples = FALSE)
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	244 #Combine the plots into one figure:
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	245 grid.arrange(pch1, pch2, ncol = 2, widths = c(2, 1.6))
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	246
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	247 # Compare the reconstructed mutational profile with the original mutational profile:
25 b00fef2b1c2c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit eeb46055822c6805c209af0c450ae941100960bd artbio parents: 24 diff changeset	248 pch3 <- plot_original_vs_reconstructed(pseudo_mut_mat, nmf_res$reconstructed, y_intercept = 0.95)
b00fef2b1c2c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit eeb46055822c6805c209af0c450ae941100960bd artbio parents: 24 diff changeset	249 grid.arrange(pch3)
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	250 dev.off()
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	251 }
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	252
18 8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	253 ##### Section 3: Find optimal contribution of known signatures: COSMIC or OWN mutational signatures ####
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	254
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	255 if (!is.na(opt$output_sigpattern)[1]) {
17 8c6ee1c2248f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e5d498dfc5a6a9aaea3d09037dea5d15c2d85dd2" artbio parents: 16 diff changeset	256 # Prepare cosmic signatures
18 8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	257 if (!is.na(opt$cosmic_version)) {
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	258 cosmic_urls <- read.delim(paste0(opt$tooldir, "cosmic_urls.tsv"), sep = "\t", header = TRUE)
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	259 cosmic_sbs_file <- cosmic_urls$url[cosmic_urls$genome == opt$genome &
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	260 cosmic_urls$cosmic_version == opt$cosmic_version]
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	261 sbs_signatures <- read.table(paste0(opt$tooldir, cosmic_sbs_file),
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	262 sep = "\t", header = TRUE)
19 69f09dff98f9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit db5fd077ec6c840b7b6eda331820999f85fd7c26" artbio parents: 18 diff changeset	263 tag <- paste(gsub("BSgenome.Hsapiens.UCSC.", "", opt$genome), "COSMIC", opt$cosmic_version, sep = " ")
18 8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	264 }
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	265 # Prepare user-defined signatures
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	266 if (!is.na(opt$own_signatures)) {
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	267 sbs_signatures <- read.table(opt$own_signatures, sep = "\t", header = TRUE)
20 a2cb7dc9250a "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit b07cf2662a36d88f80dc08ef4f46454dbc133094" artbio parents: 19 diff changeset	268 tag <- paste(gsub("BSgenome.Hsapiens.UCSC.", "", opt$genome), "User-Defined Signatures", sep = " ")
18 8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	269 }
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	270 row.names(sbs_signatures) <- sbs_signatures$Type
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	271 # drop column Type of sbs_signatures
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	272 sbs_signatures <- subset(sbs_signatures, select = -c(Type))
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	273 # reorder substitutions of sbs_signatures to match mut_mat
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	274 sbs_signatures <- sbs_signatures[match(row.names(mut_mat), row.names(sbs_signatures)), ]
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	275 # arrange signature colors
20 a2cb7dc9250a "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit b07cf2662a36d88f80dc08ef4f46454dbc133094" artbio parents: 19 diff changeset	276 if (opt$colors == "intense") {
22 00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	277 signature_colors <- c("#3f4100", "#6f53ff", "#6dc400", "#9d1fd7", "#009c06", "#001fae", "#c4bedf", "#8adb4d", "#5a67ff", "#d8c938", "#024bc3",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	278 "#d2ab00", "#e36eff", "#cad5b3", "#00ac44", "#d000b0", "#01b071", "#ff64e2", "#006b21", "#b70090", "#60dc9f", "#5f0083",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	279 "#c0ce67", "#002981", "#e6b8b3", "#ffb53e", "#44005f", "#b59600", "#7d95ff", "#f47600", "#017bc4", "#ff2722", "#02cfec",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	280 "#ff233f", "#01b7b4", "#fd005c", "#019560", "#ff57a9", "#88d896", "#b80067", "#abd27f", "#dc8eff", "#667b00", "#fba3ff",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	281 "#093f00", "#ff6494", "#009791", "#c93200", "#4ac8ff", "#a60005", "#8fd4b6", "#ce0036", "#00634d", "#ff6035", "#2d1956",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	282 "#f0be6d", "#6a0058", "#957a00", "#e4b4ff", "#4a5500", "#abc7fe", "#c95900", "#003d27", "#b10043", "#d5c68e", "#3e163e",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	283 "#b36b00", "#debaeb", "#605400", "#7a0044", "#ffa06d", "#4c0d21", "#ff9cb5", "#3f1d02", "#ff958f", "#634a66", "#775500",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	284 "#6e0028", "#717653", "#6c1000", "#693600")
20 a2cb7dc9250a "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit b07cf2662a36d88f80dc08ef4f46454dbc133094" artbio parents: 19 diff changeset	285 } else {
22 00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	286 signature_colors <- c("#7FC97F", "#BEAED4", "#FDC086", "#FFFF99", "#386CB0", "#F0027F", "#c4bedf", "#BF5B17", "#666666", "#1B9E77", "#D95F02",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	287 "#7570B3", "#E7298A", "#cad5b3", "#66A61E", "#E6AB02", "#A6761D", "#A6CEE3", "#1F78B4", "#B2DF8A", "#33A02C", "#FB9A99",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	288 "#E31A1C", "#B3E2CD", "#e6b8b3", "#FF7F00", "#CAB2D6", "#6A3D9A", "#B15928", "#FBB4AE", "#B3CDE3", "#CCEBC5", "#DECBE4",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	289 "#FED9A6", "#FFFFCC", "#E5D8BD", "#FDDAEC", "#F2F2F2", "#B3E2CD", "#FDCDAC", "#CBD5E8", "#F4CAE4", "#E6F5C9", "#FFF2AE",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	290 "#F1E2CC", "#CCCCCC", "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FFFF33", "#A65628", "#F781BF", "#999999", "#66C2A5",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	291 "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	292 "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", "#D9D9D9", "#BC80BD", "#FFED6F", "#3f1d02", "#ff958f", "#634a66", "#775500",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	293 "#6e0028", "#717653", "#6c1000", "#693600")
20 a2cb7dc9250a "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit b07cf2662a36d88f80dc08ef4f46454dbc133094" artbio parents: 19 diff changeset	294 }
22 00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	295 names(signature_colors) <- c("SBS1", "SBS2", "SBS3", "SBS4", "SBS5", "SBS6", "SBS7", "SBS7a", "SBS7b", "SBS7c", "SBS7d",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	296 "SBS8", "SBS9", "SBS10", "SBS10a", "SBS10b", "SBS10c", "SBS10d", "SBS11", "SBS12", "SBS13", "SBS14",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	297 "SBS15", "SBS16", "SBS17", "SBS17a", "SBS17b", "SBS18", "SBS19", "SBS20", "SBS21", "SBS22", "SBS23",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	298 "SBS24", "SBS25", "SBS26", "SBS27", "SBS28", "SBS29", "SBS30", "SBS31", "SBS32", "SBS33", "SBS34",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	299 "SBS35", "SBS36", "SBS37", "SBS38", "SBS39", "SBS40", "SBS41", "SBS42", "SBS43", "SBS44", "SBS45",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	300 "SBS46", "SBS47", "SBS48", "SBS49", "SBS50", "SBS51", "SBS52", "SBS53", "SBS54", "SBS55", "SBS56",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	301 "SBS57", "SBS58", "SBS59", "SBS60", "SBS84", "SBS85", "SBS86", "SBS87", "SBS88", "SBS89", "SBS90",
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	302 "SBS91", "SBS92", "SBS93", "SBS94")
00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	303
23 83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	304 # if signature names provided are not compliant with cosmic nomenclature,
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	305 # we attribute these names to the active signature_colors vector, adjusted to the length
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	306 # of the signature names.
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	307
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	308 if (! all(colnames(sbs_signatures) %in% names(signature_colors))) { # provided signature are not all included in cosmic names
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	309 signature_colors <- signature_colors[seq_along(sbs_signatures)]
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	310 names(signature_colors) <- colnames(sbs_signatures)
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	311 }
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	312
18 8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	313 # This is IMPORTANT since in Galaxy we do not use the embeded function get_known_signatures()
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	314 sbs_signatures <- as.matrix(sbs_signatures)
17 8c6ee1c2248f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e5d498dfc5a6a9aaea3d09037dea5d15c2d85dd2" artbio parents: 16 diff changeset	315
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	316
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	317 # Plot mutational profiles of the COSMIC signatures
18 8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	318
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	319 pdf(opt$output_sigpattern, paper = "special", width = 11.69, height = 11.69)
23 83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	320 if (opt$display_signatures == "yes") {
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	321 for (i in head(seq(1, ncol(sbs_signatures), by = 20), -1)) {
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	322 p6 <- plot_96_profile(sbs_signatures[, i:(i + 19)], condensed = TRUE, ymax = 0.3)
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	323 grid.arrange(p6, top = textGrob(paste0(tag, " profiles (", trunc((i + 1) / 20) + 1, " of ",
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	324 trunc(ncol(sbs_signatures) / 20) + 1, " pages)"),
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	325 gp = gpar(fontsize = 12, font = 3)))
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	326 }
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	327 p6 <- plot_96_profile(sbs_signatures[, (trunc(ncol(sbs_signatures) / 20) * 20):(ncol(sbs_signatures))],
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	328 condensed = TRUE, ymax = 0.3)
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58" artbio parents: 22 diff changeset	329 grid.arrange(p6, top = textGrob(paste0(tag, " profiles (", trunc(ncol(sbs_signatures) / 20) + 1, " of ",
18 8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	330 trunc(ncol(sbs_signatures) / 20) + 1, " pages)"),
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	331 gp = gpar(fontsize = 12, font = 3)))
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	332 }
19 69f09dff98f9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit db5fd077ec6c840b7b6eda331820999f85fd7c26" artbio parents: 18 diff changeset	333
69f09dff98f9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit db5fd077ec6c840b7b6eda331820999f85fd7c26" artbio parents: 18 diff changeset	334
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	335 # Find optimal contribution of COSMIC signatures to reconstruct 96 mutational profiles
17 8c6ee1c2248f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e5d498dfc5a6a9aaea3d09037dea5d15c2d85dd2" artbio parents: 16 diff changeset	336 pseudo_mut_mat <- mut_mat + 0.0001 # First add a small pseudocount to the mutation count matrix
18 8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	337 fit_res <- fit_to_signatures(pseudo_mut_mat, sbs_signatures)
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	338
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	339 # Plot contribution barplots
24 ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d artbio parents: 23 diff changeset	340 pc3 <- plot_contribution(fit_res$contribution, sbs_signatures, coord_flip = TRUE, mode = "absolute")
ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d artbio parents: 23 diff changeset	341 pc4 <- plot_contribution(fit_res$contribution, sbs_signatures, coord_flip = TRUE, mode = "relative")
15 8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37" artbio parents: 14 diff changeset	342 if (is.na(opt$levels)[1]) { # if there are NO levels to display in graphs
4 7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c" artbio parents: 3 diff changeset	343 pc3_data <- pc3$data
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	344 pc3 <- ggplot(pc3_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) +
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	345 geom_bar(stat = "identity", position = "stack") +
4 7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c" artbio parents: 3 diff changeset	346 coord_flip() +
22 00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	347 scale_fill_manual(name = tag, values = signature_colors[colnames(sbs_signatures)]) +
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	348 labs(x = "Samples", y = "Absolute contribution") + theme_bw() +
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	349 theme(panel.grid.minor.x = element_blank(),
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	350 panel.grid.major.x = element_blank(),
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	351 legend.position = "right",
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	352 text = element_text(size = 8),
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	353 axis.text.x = element_text(angle = 90, hjust = 1))
4 7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c" artbio parents: 3 diff changeset	354 pc4_data <- pc4$data
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	355 pc4 <- ggplot(pc4_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) +
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	356 geom_bar(stat = "identity", position = "fill") +
4 7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c" artbio parents: 3 diff changeset	357 coord_flip() +
22 00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	358 scale_fill_manual(name = tag, values = signature_colors[colnames(sbs_signatures)]) +
4 7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c" artbio parents: 3 diff changeset	359 scale_y_continuous(labels = scales::percent_format(accuracy = 1)) +
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	360 labs(x = "Samples", y = "Relative contribution") + theme_bw() +
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	361 theme(panel.grid.minor.x = element_blank(), panel.grid.major.x = element_blank(), legend.position = "right",
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	362 text = element_text(size = 8),
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	363 axis.text.x = element_text(angle = 90, hjust = 1))
15 8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37" artbio parents: 14 diff changeset	364 }
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	365 #####
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	366 # ggplot2 alternative
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	367 if (!is.na(opt$levels)[1]) { # if there are levels to display in graphs
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	368 pc3_data <- pc3$data
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	369 pc3_data <- merge(pc3_data, metadata_table[, c(1, 3)], by.x = "Sample", by.y = "element_identifier")
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	370 pc3 <- ggplot(pc3_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) +
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	371 geom_bar(stat = "identity", position = "stack") +
22 00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	372 scale_fill_manual(name = tag, values = signature_colors[colnames(sbs_signatures)]) +
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	373 labs(x = "Samples", y = "Absolute contribution") + theme_bw() +
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	374 theme(panel.grid.minor.x = element_blank(),
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	375 panel.grid.major.x = element_blank(),
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	376 legend.position = "right",
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	377 text = element_text(size = 8),
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	378 axis.text.x = element_text(angle = 90, hjust = 1)) +
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	379 facet_grid(~level, scales = "free_x", space = "free")
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	380 pc4_data <- pc4$data
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	381 pc4_data <- merge(pc4_data, metadata_table[, c(1, 3)], by.x = "Sample", by.y = "element_identifier")
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	382 pc4 <- ggplot(pc4_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) +
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	383 geom_bar(stat = "identity", position = "fill") +
22 00be8f0b2c89 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 13d907bd98700858433fc28c6bf2d92e9012bfb2" artbio parents: 21 diff changeset	384 scale_fill_manual(name = tag, values = signature_colors[colnames(sbs_signatures)]) +
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	385 scale_y_continuous(labels = scales::percent_format(accuracy = 1)) +
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	386 labs(x = "Samples", y = "Relative contribution") + theme_bw() +
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	387 theme(panel.grid.minor.x = element_blank(),
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	388 panel.grid.major.x = element_blank(),
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	389 legend.position = "right",
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	390 text = element_text(size = 8),
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	391 axis.text.x = element_text(angle = 90, hjust = 1)) +
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	392 facet_grid(~level, scales = "free_x", space = "free")
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	393 }
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	394 # Combine the two plots:
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	395 grid.arrange(pc3, pc4,
18 8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	396 top = textGrob("Absolute and Relative Contributions of elementary signatures to mutational profiles",
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	397 gp = gpar(fontsize = 12, font = 3)))
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	398
8 e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	399 #### pie charts of comic signatures contributions in samples ###
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	400 library(reshape2)
8 e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	401 library(dplyr)
e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	402 if (length(levels(factor(levels_table$level))) < 2) {
e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	403 fit_res_contrib <- as.data.frame(fit_res$contribution)
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	404 worklist <- cbind(signature = rownames(fit_res$contribution),
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	405 level = rep("nolabels", length(fit_res_contrib[, 1])),
8 e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	406 fit_res_contrib,
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	407 sum = rowSums(fit_res_contrib))
24 ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d artbio parents: 23 diff changeset	408 worklist <- worklist[order(worklist[, "sum"], decreasing = TRUE), ]
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	409 worklist <- worklist[1:opt$signum, ]
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	410 worklist <- worklist[, -length(worklist[1, ])]
8 e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	411 worklist <- melt(worklist)
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	412 worklist <- worklist[, c(1, 3, 4, 2)]
8 e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	413 } else {
e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	414 worklist <- list()
e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	415 for (i in levels(factor(levels_table$level))) {
24 ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d artbio parents: 23 diff changeset	416 worklist[[i]] <- fit_res$contribution[, levels_table$element_identifier[levels_table$level == i]]
8 e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	417 sum <- rowSums(as.data.frame(worklist[[i]]))
e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	418 worklist[[i]] <- cbind(worklist[[i]], sum)
24 ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d artbio parents: 23 diff changeset	419 worklist[[i]] <- worklist[[i]][order(worklist[[i]][, "sum"], decreasing = TRUE), ]
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	420 worklist[[i]] <- worklist[[i]][1:opt$signum, ]
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	421 worklist[[i]] <- worklist[[i]][, -length(as.data.frame(worklist[[i]]))]
8 e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	422 }
e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	423 worklist <- as.data.frame(melt(worklist))
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	424 worklist[, 2] <- paste0(worklist[, 4], " - ", worklist[, 2])
8 e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	425 }
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	426
8 e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	427 colnames(worklist) <- c("signature", "sample", "value", "level")
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	428 worklist <- as.data.frame(worklist %>% group_by(sample) %>% mutate(value = value / sum(value) * 100))
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	429 worklist$pos <- cumsum(worklist$value) - worklist$value / 2
21 8a5aaa97dbd6 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 91415d0273efacfc605199a8fbebaf421da9df7e" artbio parents: 20 diff changeset	430 worklist$label <- factor(gsub("SBS", "", worklist$signature))
8 e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	431 worklist$signature <- factor(worklist$signature)
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	432 p7 <- ggplot(worklist, aes(x = "", y = value, group = signature, fill = signature)) +
8 e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	433 geom_bar(width = 1, stat = "identity") +
21 8a5aaa97dbd6 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 91415d0273efacfc605199a8fbebaf421da9df7e" artbio parents: 20 diff changeset	434 geom_text(aes(label = label), position = position_stack(vjust = 0.5), color = "white", size = 3) +
24 ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d artbio parents: 23 diff changeset	435 coord_polar("y", start = 0) + facet_wrap(. ~ sample) +
18 8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	436 labs(x = "", y = "Samples", fill = tag) +
8 e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	437 scale_fill_manual(name = paste0(opt$signum, " most contributing\nsignatures\n(in each label/tissue)"),
18 8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	438 values = signature_colors[levels(worklist$signature)],
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	439 labels = names(signature_colors[levels(worklist$signature)])) +
8 e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	440 theme(axis.text = element_blank(),
e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	441 axis.ticks = element_blank(),
e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710" artbio parents: 7 diff changeset	442 panel.grid = element_blank())
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	443 grid.arrange(p7)
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	444
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	445 # Plot relative contribution of the cancer signatures in each sample as a heatmap with sample clustering
4 7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c" artbio parents: 3 diff changeset	446 if (length(vcf_paths) > 1) {
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c" artbio parents: 3 diff changeset	447 p8 <- plot_contribution_heatmap(fit_res$contribution, cluster_samples = TRUE, method = "complete")
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c" artbio parents: 3 diff changeset	448 grid.arrange(p8)
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c" artbio parents: 3 diff changeset	449 }
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	450
11 7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460" artbio parents: 10 diff changeset	451 # export relative contribution matrix
7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460" artbio parents: 10 diff changeset	452 if (!is.na(opt$sig_contrib_matrix)) {
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	453 output_table <- t(fit_res$contribution) / rowSums(t(fit_res$contribution))
12 7954f0d3517f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 7c990ad7024035342c4abd6e3fa8feb1b2f2ac2c" artbio parents: 11 diff changeset	454 if (length(levels(factor(levels_table$level))) > 1) {
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	455 output_table <- data.frame(sample = paste0(metadata_table[metadata_table$element_identifier == colnames(fit_res$contribution),
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	456 3], "-", colnames(fit_res$contribution)),
13 6741b819cc15 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 372eb902f528baa8b5465b83d992a1d146343dfe" artbio parents: 12 diff changeset	457 output_table)
18 8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	458 colnames(output_table) <- gsub("X", "SBS", colnames(output_table))
12 7954f0d3517f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 7c990ad7024035342c4abd6e3fa8feb1b2f2ac2c" artbio parents: 11 diff changeset	459 } else {
18 8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	460 output_table <- data.frame(sample = rownames(output_table), output_table)
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	461 colnames(output_table) <- gsub("X", "SBS", colnames(output_table))
12 7954f0d3517f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 7c990ad7024035342c4abd6e3fa8feb1b2f2ac2c" artbio parents: 11 diff changeset	462 }
24 ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d artbio parents: 23 diff changeset	463 write.table(output_table, file = opt$sig_contrib_matrix, sep = "\t", quote = FALSE, row.names = FALSE)
11 7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460" artbio parents: 10 diff changeset	464 }
7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460" artbio parents: 10 diff changeset	465
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	466 # calculate all pairwise cosine similarities
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	467 cos_sim_ori_rec <- cos_sim_matrix(pseudo_mut_mat, fit_res$reconstructed)
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	468 # extract cosine similarities per sample between original and reconstructed
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	469 cos_sim_ori_rec <- as.data.frame(diag(cos_sim_ori_rec))
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	470
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	471 # We can use ggplot to make a barplot of the cosine similarities between the original and
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	472 # reconstructed mutational profile of each sample. This clearly shows how well each mutational
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	473 # profile can be reconstructed with the COSMIC mutational signatures. Two identical profiles
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	474 # have a cosine similarity of 1. The lower the cosine similarity between original and
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	475 # reconstructed, the less well the original mutational profile can be reconstructed with
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	476 # the COSMIC signatures. You could use, for example, cosine similarity of 0.95 as a cutoff.
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	477
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	478 # Adjust data frame for plotting with gpplot
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	479 colnames(cos_sim_ori_rec) <- "cos_sim"
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	480 cos_sim_ori_rec$sample <- row.names(cos_sim_ori_rec)
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	481 # Make barplot
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	482 p9 <- ggplot(cos_sim_ori_rec, aes(y = cos_sim, x = sample)) +
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	483 geom_bar(stat = "identity", fill = "skyblue4") +
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	484 coord_cartesian(ylim = c(0.8, 1)) +
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	485 # coord_flip(ylim=c(0.8,1)) +
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	486 ylab("Cosine similarity\n original VS reconstructed") +
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	487 xlab("") +
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	488 # Reverse order of the samples such that first is up
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	489 # xlim(rev(levels(factor(cos_sim_ori_rec$sample)))) +
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	490 theme_bw() +
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	491 theme(panel.grid.minor.y = element_blank(),
26 af5c65ad5317 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bc7fab3050541155f0c3e15b7f448a1802155670 artbio parents: 25 diff changeset	492 panel.grid.major.y = element_blank(),
af5c65ad5317 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bc7fab3050541155f0c3e15b7f448a1802155670 artbio parents: 25 diff changeset	493 axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1)
af5c65ad5317 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bc7fab3050541155f0c3e15b7f448a1802155670 artbio parents: 25 diff changeset	494 ) +
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	495 # Add cut.off line
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	496 geom_hline(aes(yintercept = .95))
18 8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430" artbio parents: 17 diff changeset	497 grid.arrange(p9, top = textGrob("Similarity between true profiles and profiles reconstructed with elementary signatures", gp = gpar(fontsize = 12, font = 3)))
2 aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	498 dev.off()
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419" artbio parents: 0 diff changeset	499 }
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	500
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	501
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	502 # Output RData file
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	503 if (!is.null(opt$rdata)) {
14 56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3" artbio parents: 13 diff changeset	504 save.image(file = opt$rdata)
3 e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f" artbio parents: 2 diff changeset	505 }

Mercurial > repos > artbio > mutational_patterns

annotate mutational_patterns.R @ 26:af5c65ad5317 draft