Mercurial > repos > artbio > mutational_patterns

annotate mutational_patterns.R @ 11:7995a949189f draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460"
author artbio
date Thu, 22 Oct 2020 00:18:38 +0000
parents 59c0e2a7965c
children 7954f0d3517f
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924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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diff changeset
1 # load packages that are provided in the conda env
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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2 options( show.error.messages=F,
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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3 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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4 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
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5 warnings()
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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6 library(optparse)
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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7 library(rjson)
2
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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8 library(grid)
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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9 library(gridExtra)
4
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
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10 library(scales)
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
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11 library(RColorBrewer)
0
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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12
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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13 # Arguments
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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14 option_list = list(
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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15 make_option(
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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16 "--inputs",
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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17 default = NA,
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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18 type = 'character',
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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19 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"
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20 ),
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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21 make_option(
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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22 "--genome",
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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23 default = NA,
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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24 type = 'character',
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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25 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
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26 ),
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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27 make_option(
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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28 "--levels",
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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29 default = NA,
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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30 type = 'character',
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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31 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
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32 ),
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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33 make_option(
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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34 "--cosmic_version",
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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35 default = "v2",
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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36 type = 'character',
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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37 help = "Version of the Cosmic Signature set to be used to express mutational patterns"
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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38 ),
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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39 make_option(
0
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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40 "--signum",
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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41 default = 2,
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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42 type = 'integer',
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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43 help = "selects the N most significant signatures in samples to express mutational patterns"
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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44 ),
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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45 make_option(
2
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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46 "--nrun",
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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47 default = 2,
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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48 type = 'integer',
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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49 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
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50 ),
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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diff changeset
51 make_option(
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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diff changeset
52 "--rank",
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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diff changeset
53 default = 2,
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 0
diff changeset
54 type = 'integer',
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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55 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
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56 ),
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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57 make_option(
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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diff changeset
58 "--newsignum",
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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diff changeset
59 default = 2,
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 0
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60 type = 'integer',
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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61 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
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62 ),
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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63 make_option(
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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diff changeset
64 "--output_spectrum",
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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65 default = NA,
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 0
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66 type = 'character',
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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67 help = "path to output dataset"
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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68 ),
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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diff changeset
69 make_option(
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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70 "--output_denovo",
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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71 default = NA,
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 0
diff changeset
72 type = 'character',
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 0
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73 help = "path to output dataset"
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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74 ),
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 0
diff changeset
75 make_option(
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
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76 "--sigmatrix",
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
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77 default = NA,
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
78 type = 'character',
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
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79 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
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80 ),
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
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81 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
82 "--output_cosmic",
0
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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83 default = NA,
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
84 type = 'character',
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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85 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
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86 ),
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
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87 make_option(
11
7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460"
artbio
parents: 10
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88 "--sig_contrib_matrix",
7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460"
artbio
parents: 10
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89 default = NA,
7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460"
artbio
parents: 10
diff changeset
90 type = 'character',
7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460"
artbio
parents: 10
diff changeset
91 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
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92 ),
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93 make_option(
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94 c("-r", "--rdata"),
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95 type="character",
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96 default=NULL,
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97 help="Path to RData output file")
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98 )
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99
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100 opt = parse_args(OptionParser(option_list = option_list),
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101 args = commandArgs(trailingOnly = TRUE))
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102
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103 ################ Manage input data ####################
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104 json_dict <- opt$inputs
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105 parser <- newJSONParser()
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106 parser$addData(json_dict)
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107 fileslist <- parser$getObject()
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108 vcf_paths <- attr(fileslist, "names")
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109 element_identifiers <- unname(unlist(fileslist))
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110 ref_genome <- opt$genome
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111 vcf_table <- data.frame(element_identifier=as.character(element_identifiers), path=vcf_paths)
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112
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113 library(MutationalPatterns)
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114 library(ref_genome, character.only = TRUE)
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115 library(ggplot2)
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116
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117 # Load the VCF files into a GRangesList:
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118 vcfs <- read_vcfs_as_granges(vcf_paths, element_identifiers, ref_genome)
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119 library(plyr)
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120 if (!is.na(opt$levels)[1]) { # manage levels if there are
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121 levels_table <- read.delim(opt$levels, header=FALSE, col.names=c("element_identifier","level"))
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122 } else {
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123 levels_table <- data.frame(element_identifier=vcf_table$element_identifier,
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124 level=rep("nolabels", length(vcf_table$element_identifier)))
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125 }
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126 metadata_table <- join(vcf_table, levels_table, by = "element_identifier")
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127 tissue <- as.vector(metadata_table$level)
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128 detach(package:plyr)
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129
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130 ##### This is done for any section ######
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131 mut_mat <- mut_matrix(vcf_list = vcfs, ref_genome = ref_genome)
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132 qual_col_pals = brewer.pal.info[brewer.pal.info$category == 'qual',]
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133 col_vector = unique(unlist(mapply(brewer.pal, qual_col_pals$maxcolors, rownames(qual_col_pals))))
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134 col_vector <- col_vector[c(-32, -34, -39)] # 67-color palette
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135
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136 ###### Section 1 Mutation characteristics and spectrums #############
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137 if (!is.na(opt$output_spectrum)[1]) {
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138 pdf(opt$output_spectrum, paper = "special", width = 11.69, height = 11.69)
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139 type_occurrences <- mut_type_occurrences(vcfs, ref_genome)
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140
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141 # mutation spectrum, total or by sample
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142
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143 if (length(levels(factor(levels_table$level))) == 1) { # (is.na(opt$levels)[1])
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144 p1 <- plot_spectrum(type_occurrences, CT = TRUE, legend=TRUE)
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145 plot(p1)
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146 } else {
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147 p2 <- plot_spectrum(type_occurrences, by = tissue, CT=TRUE) # by levels
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148 p3 <- plot_spectrum(type_occurrences, CT=TRUE, legend=TRUE) # total
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149 grid.arrange(p2, p3, ncol=2, widths=c(4,2.3), heights=c(4,1))
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150 }
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151 plot_96_profile(mut_mat, condensed = TRUE)
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152 dev.off()
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153 }
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154
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155 ###### Section 2: De novo mutational signature extraction using NMF #######
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156 if (!is.na(opt$output_denovo)[1]) {
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157 # opt$rank cannot be higher than the number of samples
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158 if (opt$rank > length(element_identifiers)) {opt$rank <-length(element_identifiers)}
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159 # likewise, opt$signum cannot be higher thant the number of samples
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160 if (opt$signum > length(element_identifiers)) {opt$signum <-length(element_identifiers)}
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161 pseudo_mut_mat <- mut_mat + 0.0001 # First add a small pseudocount to the mutation count matrix
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162 # Use the NMF package to generate an estimate rank plot
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163 library("NMF")
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164 estimate <- nmf(pseudo_mut_mat, rank=1:opt$rank, method="brunet", nrun=opt$nrun, seed=123456)
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165 # And plot it
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166 pdf(opt$output_denovo, paper = "special", width = 11.69, height = 11.69)
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167 p4 <- plot(estimate)
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168 grid.arrange(p4)
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169 # Extract 4 (PARAMETIZE) mutational signatures from the mutation count matrix with extract_signatures
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170 # (For larger datasets it is wise to perform more iterations by changing the nrun parameter
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171 # to achieve stability and avoid local minima)
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172 nmf_res <- extract_signatures(pseudo_mut_mat, rank=opt$newsignum, nrun=opt$nrun)
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173 # Assign signature names
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174 colnames(nmf_res$signatures) <- paste0("NewSig_", 1:opt$newsignum)
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175 rownames(nmf_res$contribution) <- paste0("NewSig_", 1:opt$newsignum)
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176 # Plot the 96-profile of the signatures:
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177 p5 <- plot_96_profile(nmf_res$signatures, condensed = TRUE)
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178 new_sig_matrix <- reshape2::dcast(p5$data, substitution + context ~ variable, value.var = "value")
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179 new_sig_matrix = format(new_sig_matrix, scientific=TRUE)
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180 write.table(new_sig_matrix, file=opt$sigmatrix, quote = FALSE, row.names = FALSE, sep="\t")
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181 grid.arrange(p5)
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182 # Visualize the contribution of the signatures in a barplot
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183 pc1 <- plot_contribution(nmf_res$contribution, nmf_res$signature, mode="relative", coord_flip = TRUE)
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184 # Visualize the contribution of the signatures in absolute number of mutations
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185 pc2 <- plot_contribution(nmf_res$contribution, nmf_res$signature, mode="absolute", coord_flip = TRUE)
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186 # Combine the two plots:
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187 grid.arrange(pc1, pc2)
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188
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189 # The relative contribution of each signature for each sample can also be plotted as a heatmap with
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190 # plot_contribution_heatmap, which might be easier to interpret and compare than stacked barplots.
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191 # The samples can be hierarchically clustered based on their euclidean dis- tance. The signatures
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192 # can be plotted in a user-specified order.
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193 # Plot signature contribution as a heatmap with sample clustering dendrogram and a specified signature order:
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194 pch1 <- plot_contribution_heatmap(nmf_res$contribution,
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195 sig_order = paste0("NewSig_", 1:opt$newsignum))
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196 # Plot signature contribution as a heatmap without sample clustering:
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197 pch2 <- plot_contribution_heatmap(nmf_res$contribution, cluster_samples=FALSE)
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198 #Combine the plots into one figure:
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199 grid.arrange(pch1, pch2, ncol = 2, widths = c(2,1.6))
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200
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201 # Compare the reconstructed mutational profile with the original mutational profile:
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202 plot_compare_profiles(pseudo_mut_mat[,1],
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203 nmf_res$reconstructed[,1],
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204 profile_names = c("Original", "Reconstructed"),
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205 condensed = TRUE)
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206 dev.off()
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207 }
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208 ##### Section 3: Find optimal contribution of known signatures: COSMIC mutational signatures ####
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209
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210 if (!is.na(opt$output_cosmic)[1]) {
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211 pdf(opt$output_cosmic, paper = "special", width = 11.69, height = 11.69)
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212 pseudo_mut_mat <- mut_mat + 0.0001 # First add a small psuedocount to the mutation count matrix
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213 if (opt$cosmic_version == "v2") {
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214 sp_url <- paste("https://cancer.sanger.ac.uk/cancergenome/assets/", "signatures_probabilities.txt", sep = "")
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215 cancer_signatures = read.table(sp_url, sep = "\t", header = TRUE)
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216 new_order = match(row.names(pseudo_mut_mat), cancer_signatures$Somatic.Mutation.Type)
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217 cancer_signatures = cancer_signatures[as.vector(new_order),]
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218 row.names(cancer_signatures) = cancer_signatures$Somatic.Mutation.Type
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219 cancer_signatures = as.matrix(cancer_signatures[,4:33])
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220 colnames(cancer_signatures) <- gsub("Signature.", "", colnames(cancer_signatures)) # shorten signature labels
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221 cosmic_tag <- "Signatures (Cosmic v2, March 2015)"
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222 cosmic_colors <- col_vector[1:30]
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223 } else {
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224 sp_url <- "https://raw.githubusercontent.com/ARTbio/startbio/master/sigProfiler_SBS_signatures_2019_05_22.tsv"
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225 cancer_signatures = read.table(sp_url, sep = "\t", header = TRUE)
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226 new_order = match(row.names(pseudo_mut_mat), cancer_signatures$Somatic.Mutation.Type)
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227 cancer_signatures = cancer_signatures[as.vector(new_order),]
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228 row.names(cancer_signatures) = cancer_signatures$Somatic.Mutation.Type
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229 cancer_signatures = as.matrix(cancer_signatures[,4:70])
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230 colnames(cancer_signatures) <- gsub("SBS", "", colnames(cancer_signatures)) # shorten signature labels
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231 cosmic_tag <- "Signatures (Cosmic v3, May 2019)"
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232 cosmic_colors <- col_vector[1:67]
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233 }
2
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234
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235 # Plot mutational profiles of the COSMIC signatures
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236 if (opt$cosmic_version == "v2") {
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237 p6 <- plot_96_profile(cancer_signatures, condensed = TRUE, ymax = 0.3)
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238 grid.arrange(p6, top = textGrob("COSMIC signature profiles",gp=gpar(fontsize=12,font=3)))
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239 } else {
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240 p6 <- plot_96_profile(cancer_signatures[,1:33], condensed = TRUE, ymax = 0.3)
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241 p6bis <- plot_96_profile(cancer_signatures[,34:67], condensed = TRUE, ymax = 0.3)
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242 grid.arrange(p6, top = textGrob("COSMIC signature profiles (on two pages)",gp=gpar(fontsize=12,font=3)))
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243 grid.arrange(p6bis, top = textGrob("COSMIC signature profiles (continued)",gp=gpar(fontsize=12,font=3)))
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244 }
2
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245
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246
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247 # Find optimal contribution of COSMIC signatures to reconstruct 96 mutational profiles
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248 fit_res <- fit_to_signatures(pseudo_mut_mat, cancer_signatures)
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249
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250 # Plot contribution barplots
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251 pc3 <- plot_contribution(fit_res$contribution, cancer_signatures, coord_flip = T, mode = "absolute")
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252 pc4 <- plot_contribution(fit_res$contribution, cancer_signatures, coord_flip = T, mode = "relative")
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253 pc3_data <- pc3$data
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254 pc3 <- ggplot(pc3_data, aes(x=Sample, y=Contribution, fill=as.factor(Signature))) +
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255 geom_bar(stat="identity", position='stack') +
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256 coord_flip() +
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257 scale_fill_manual(name = "Cosmic\nSignatures", values = cosmic_colors) +
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artbio
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258 labs(x = "Samples", y = "Absolute contribution") + theme_bw() +
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artbio
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diff changeset
259 theme(panel.grid.minor.x = element_blank(), panel.grid.major.x = element_blank(), legend.position="right",
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artbio
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diff changeset
260 text = element_text(size=8),
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artbio
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diff changeset
261 axis.text.x = element_text(angle=90, hjust=1))
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artbio
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diff changeset
262 pc4_data <- pc4$data
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artbio
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diff changeset
263 pc4 <- ggplot(pc4_data, aes(x=Sample, y=Contribution, fill=as.factor(Signature))) +
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artbio
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diff changeset
264 geom_bar(stat="identity", position='fill') +
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artbio
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diff changeset
265 coord_flip() +
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artbio
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diff changeset
266 scale_fill_manual(name = "Cosmic\nSignatures", values = cosmic_colors) +
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artbio
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diff changeset
267 scale_y_continuous(labels = scales::percent_format(accuracy = 1)) +
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artbio
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268 labs(x = "Samples", y = "Relative contribution") + theme_bw() +
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artbio
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diff changeset
269 theme(panel.grid.minor.x = element_blank(), panel.grid.major.x = element_blank(), legend.position="right",
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artbio
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270 text = element_text(size=8),
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artbio
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diff changeset
271 axis.text.x = element_text(angle=90, hjust=1))
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artbio
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272 #####
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artbio
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273 # ggplot2 alternative
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artbio
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274 if (!is.na(opt$levels)[1]) { # if there are levels to display in graphs
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artbio
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275 pc3_data <- pc3$data
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artbio
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276 pc3_data <- merge (pc3_data, metadata_table[,c(1,3)], by.x="Sample", by.y="element_identifier")
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artbio
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diff changeset
277 pc3 <- ggplot(pc3_data, aes(x=Sample, y=Contribution, fill=as.factor(Signature))) +
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artbio
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278 geom_bar(stat="identity", position='stack') +
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artbio
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diff changeset
279 scale_fill_manual(name = "Cosmic\nSignatures", values = cosmic_colors) +
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artbio
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280 labs(x = "Samples", y = "Absolute contribution") + theme_bw() +
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artbio
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diff changeset
281 theme(panel.grid.minor.x = element_blank(), panel.grid.major.x = element_blank(), legend.position="right",
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artbio
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diff changeset
282 text = element_text(size=8),
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artbio
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diff changeset
283 axis.text.x = element_text(angle=90, hjust=1)) +
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artbio
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diff changeset
284 facet_grid(~level, scales = "free_x", space="free")
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artbio
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diff changeset
285 pc4_data <- pc4$data
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artbio
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diff changeset
286 pc4_data <- merge (pc4_data, metadata_table[,c(1,3)], by.x="Sample", by.y="element_identifier")
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artbio
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diff changeset
287 pc4 <- ggplot(pc4_data, aes(x=Sample, y=Contribution, fill=as.factor(Signature))) +
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artbio
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288 geom_bar(stat="identity", position='fill') +
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artbio
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diff changeset
289 scale_fill_manual(name = "Cosmic\nSignatures", values = cosmic_colors) +
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artbio
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290 scale_y_continuous(labels = scales::percent_format(accuracy = 1)) +
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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291 labs(x = "Samples", y = "Relative contribution") + theme_bw() +
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artbio
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diff changeset
292 theme(panel.grid.minor.x = element_blank(), panel.grid.major.x = element_blank(), legend.position="right",
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artbio
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293 text = element_text(size=8),
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artbio
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294 axis.text.x = element_text(angle=90, hjust=1)) +
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artbio
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295 facet_grid(~level, scales = "free_x", space="free")
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artbio
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diff changeset
296 }
2
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297 # Combine the two plots:
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298 grid.arrange(pc3, pc4, top = textGrob("Absolute and Relative Contributions of Cosmic signatures to mutational patterns",gp=gpar(fontsize=12,font=3)))
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artbio
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299
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300 #### pie charts of comic signatures contributions in samples ###
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artbio
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301 library(reshape2)
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artbio
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diff changeset
302 library(dplyr)
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artbio
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diff changeset
303 if (length(levels(factor(levels_table$level))) < 2) {
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artbio
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diff changeset
304 fit_res_contrib <- as.data.frame(fit_res$contribution)
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artbio
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diff changeset
305 worklist <- cbind(signature=rownames(fit_res$contribution),
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artbio
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diff changeset
306 level=rep("nolabels", length(fit_res_contrib[,1])),
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artbio
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diff changeset
307 fit_res_contrib,
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artbio
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diff changeset
308 sum=rowSums(fit_res_contrib))
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artbio
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diff changeset
309 worklist <- worklist[order(worklist[ ,"sum"], decreasing = T), ]
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artbio
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diff changeset
310 worklist <- worklist[1:opt$signum,]
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artbio
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diff changeset
311 worklist <- worklist[ , -length(worklist[1,])]
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artbio
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diff changeset
312 worklist <- melt(worklist)
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artbio
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diff changeset
313 worklist <- worklist[,c(1,3,4,2)]
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diff changeset
314 } else {
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artbio
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diff changeset
315 worklist <- list()
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artbio
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diff changeset
316 for (i in levels(factor(levels_table$level))) {
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artbio
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diff changeset
317 fit_res$contribution[,levels_table$element_identifier[levels_table$level == i]] -> worklist[[i]]
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artbio
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diff changeset
318 sum <- rowSums(as.data.frame(worklist[[i]]))
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artbio
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diff changeset
319 worklist[[i]] <- cbind(worklist[[i]], sum)
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artbio
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diff changeset
320 worklist[[i]] <- worklist[[i]][order(worklist[[i]][ ,"sum"], decreasing = T), ]
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artbio
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diff changeset
321 worklist[[i]] <- worklist[[i]][1:opt$signum,]
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artbio
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diff changeset
322 worklist[[i]] <- worklist[[i]][ , -length(as.data.frame(worklist[[i]]))]
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artbio
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diff changeset
323 }
e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710"
artbio
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diff changeset
324 worklist <- as.data.frame(melt(worklist))
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artbio
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diff changeset
325 worklist[,2] <- paste0(worklist[,4], " - ", worklist[,2])
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artbio
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diff changeset
326 head(worklist)
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artbio
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diff changeset
327 }
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artbio
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diff changeset
328
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artbio
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diff changeset
329 colnames(worklist) <- c("signature", "sample", "value", "level")
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artbio
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diff changeset
330 worklist <- as.data.frame(worklist %>% group_by(sample) %>% mutate(value=value/sum(value)*100))
e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710"
artbio
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diff changeset
331 worklist$pos <- cumsum(worklist$value) - worklist$value/2
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artbio
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diff changeset
332 worklist$label <- factor(worklist$signature)
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artbio
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diff changeset
333 worklist$signature <- factor(worklist$signature)
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artbio
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diff changeset
334 p7 <- ggplot(worklist, aes(x="", y=value, group=signature, fill=signature)) +
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artbio
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diff changeset
335 geom_bar(width = 1, stat = "identity") +
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artbio
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diff changeset
336 geom_text(aes(label = label), position = position_stack(vjust = 0.5), color="black", size=3) +
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artbio
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diff changeset
337 coord_polar("y", start=0) + facet_wrap(.~sample) +
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artbio
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338 labs(x="", y="Samples", fill = cosmic_tag) +
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339 scale_fill_manual(name = paste0(opt$signum, " most contributing\nsignatures\n(in each label/tissue)"),
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340 values = cosmic_colors[as.numeric(levels(factor(worklist$label)))]) +
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341 theme(axis.text = element_blank(),
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342 axis.ticks = element_blank(),
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343 panel.grid = element_blank())
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344 grid.arrange(p7)
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345
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346 # Plot relative contribution of the cancer signatures in each sample as a heatmap with sample clustering
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347 if (length(vcf_paths) > 1) {
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348 p8 <- plot_contribution_heatmap(fit_res$contribution, cluster_samples = TRUE, method = "complete")
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349 grid.arrange(p8)
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350 }
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351
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352 # export relative contribution matrix
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353 if (!is.na(opt$sig_contrib_matrix)) {
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354 output_table <- t(fit_res$contribution)/rowSums(t(fit_res$contribution))
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355 colnames(output_table) <- paste0("s", colnames(output_table))
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356 output_table <- data.frame(sample=rownames(output_table), output_table)
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357 write.table(output_table, file = opt$sig_contrib_matrix, sep = "\t", quote = F, row.names = F)
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358 }
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359
2
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360 # calculate all pairwise cosine similarities
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361 cos_sim_ori_rec <- cos_sim_matrix(pseudo_mut_mat, fit_res$reconstructed)
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362 # extract cosine similarities per sample between original and reconstructed
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363 cos_sim_ori_rec <- as.data.frame(diag(cos_sim_ori_rec))
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364
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365 # We can use ggplot to make a barplot of the cosine similarities between the original and
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366 # reconstructed mutational profile of each sample. This clearly shows how well each mutational
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367 # profile can be reconstructed with the COSMIC mutational signatures. Two identical profiles
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368 # have a cosine similarity of 1. The lower the cosine similarity between original and
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369 # reconstructed, the less well the original mutational profile can be reconstructed with
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370 # the COSMIC signatures. You could use, for example, cosine similarity of 0.95 as a cutoff.
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371
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372 # Adjust data frame for plotting with gpplot
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373 colnames(cos_sim_ori_rec) = "cos_sim"
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374 cos_sim_ori_rec$sample = row.names(cos_sim_ori_rec)
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375 # Make barplot
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376 p9 <- ggplot(cos_sim_ori_rec, aes(y=cos_sim, x=sample)) +
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377 geom_bar(stat="identity", fill = "skyblue4") +
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378 coord_cartesian(ylim=c(0.8, 1)) +
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379 # coord_flip(ylim=c(0.8,1)) +
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380 ylab("Cosine similarity\n original VS reconstructed") +
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381 xlab("") +
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382 # Reverse order of the samples such that first is up
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383 # xlim(rev(levels(factor(cos_sim_ori_rec$sample)))) +
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384 theme_bw() +
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385 theme(panel.grid.minor.y=element_blank(),
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386 panel.grid.major.y=element_blank()) +
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387 # Add cut.off line
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388 geom_hline(aes(yintercept=.95))
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389 grid.arrange(p9, top = textGrob("Similarity between true and reconstructed profiles (with all Cosmic sig.)",gp=gpar(fontsize=12,font=3)))
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390 dev.off()
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391 }
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392
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393
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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394 # Output RData file
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395 if (!is.null(opt$rdata)) {
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396 save.image(file=opt$rdata)
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397 }