Mercurial > repos > artbio > mutational_patterns

annotate mutational_patterns.R @ 3:e332cf9dfa06 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
author artbio
date Thu, 24 Sep 2020 01:32:52 +0000
parents aea952be68cb
children 7ba08c826888
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0
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"
artbio
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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"
artbio
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9 library(gridExtra)
0
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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10
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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11 # Arguments
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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12 option_list = list(
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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13 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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14 "--inputs",
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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15 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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16 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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17 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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18 ),
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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19 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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20 "--genome",
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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21 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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22 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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23 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"
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24 ),
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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25 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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26 "--levels",
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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27 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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28 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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29 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"
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30 ),
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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31 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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32 "--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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33 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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34 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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35 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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36 ),
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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37 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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38 "--signum",
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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39 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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40 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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41 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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42 ),
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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43 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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44 "--nrun",
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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45 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
46 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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47 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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48 ),
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
49 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
50 "--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
51 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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52 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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53 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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54 ),
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
55 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
56 "--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
57 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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58 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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59 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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60 ),
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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61 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
62 "--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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63 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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64 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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65 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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66 ),
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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67 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
68 "--output_denovo",
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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69 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
70 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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71 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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72 ),
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 0
diff changeset
73 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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74 "--sigmatrix",
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
75 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
76 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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77 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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78 ),
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
79 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
80 "--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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81 default = NA,
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
82 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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83 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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84 ),
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
85 make_option(
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 c("-r", "--rdata"),
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 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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88 default=NULL,
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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89 help="Path to RData output file")
0
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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90 )
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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91
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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92 opt = parse_args(OptionParser(option_list = option_list),
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93 args = commandArgs(trailingOnly = TRUE))
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94
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95 ################ Manage input data ####################
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96 json_dict <- opt$inputs
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97 parser <- newJSONParser()
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98 parser$addData(json_dict)
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99 fileslist <- parser$getObject()
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100 vcf_paths <- attr(fileslist, "names")
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101 element_identifiers <- unname(unlist(fileslist))
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102 ref_genome <- opt$genome
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103 vcf_table <- data.frame(element_identifier=element_identifiers, path=vcf_paths)
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104
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105 library(MutationalPatterns)
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106 library(ref_genome, character.only = TRUE)
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107 library(ggplot2)
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108
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109 # Load the VCF files into a GRangesList:
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110 vcfs <- read_vcfs_as_granges(vcf_paths, element_identifiers, ref_genome)
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111 if (!is.na(opt$levels)[1]) { # manage levels if there are
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112 levels_table <- read.delim(opt$levels, header=FALSE, col.names=c("element_identifier","level"))
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113 library(plyr)
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114 metadata_table <- join(vcf_table, levels_table, by = "element_identifier")
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115 tissue <- as.vector(metadata_table$level)
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116 }
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117
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118 ##### This is done for any section ######
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119 mut_mat <- mut_matrix(vcf_list = vcfs, ref_genome = ref_genome)
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120
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121 ###### Section 1 Mutation characteristics and spectrums #############
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122 if (!is.na(opt$output_spectrum)[1]) {
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123 pdf(opt$output_spectrum, paper = "special", width = 11.69, height = 11.69)
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124 type_occurrences <- mut_type_occurrences(vcfs, ref_genome)
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125
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126 # mutation spectrum, total or by sample
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127
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128 if (is.na(opt$levels)[1]) {
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129 p1 <- plot_spectrum(type_occurrences, CT = TRUE, legend=TRUE)
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130 plot(p1)
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131 } else {
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132 p2 <- plot_spectrum(type_occurrences, by = tissue, CT=TRUE) # by levels
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133 p3 <- plot_spectrum(type_occurrences, CT=TRUE, legend=TRUE) # total
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134 grid.arrange(p2, p3, ncol=2, widths=c(4,2.3), heights=c(4,1))
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135 }
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136 plot_96_profile(mut_mat, condensed = TRUE)
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137 dev.off()
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138 }
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139
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140 ###### Section 2: De novo mutational signature extraction using NMF #######
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141 if (!is.na(opt$output_denovo)[1]) {
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142 # opt$rank cannot be higher than the number of samples
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143 if (opt$rank > length(element_identifiers)) {opt$rank <-length(element_identifiers)}
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144 # likewise, opt$signum cannot be higher thant the number of samples
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145 if (opt$signum > length(element_identifiers)) {opt$signum <-length(element_identifiers)}
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146 pseudo_mut_mat <- mut_mat + 0.0001 # First add a small pseudocount to the mutation count matrix
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147 # Use the NMF package to generate an estimate rank plot
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148 library("NMF")
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149 estimate <- nmf(pseudo_mut_mat, rank=1:opt$rank, method="brunet", nrun=opt$nrun, seed=123456)
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150 # And plot it
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151 pdf(opt$output_denovo, paper = "special", width = 11.69, height = 11.69)
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152 p4 <- plot(estimate)
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153 grid.arrange(p4)
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154 # Extract 4 (PARAMETIZE) mutational signatures from the mutation count matrix with extract_signatures
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155 # (For larger datasets it is wise to perform more iterations by changing the nrun parameter
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156 # to achieve stability and avoid local minima)
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157 nmf_res <- extract_signatures(pseudo_mut_mat, rank=opt$newsignum, nrun=opt$nrun)
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158 # Assign signature names
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159 colnames(nmf_res$signatures) <- paste0("NewSig_", 1:opt$newsignum)
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160 rownames(nmf_res$contribution) <- paste0("NewSig_", 1:opt$newsignum)
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161 # Plot the 96-profile of the signatures:
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162 p5 <- plot_96_profile(nmf_res$signatures, condensed = TRUE)
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163 new_sig_matrix <- reshape2::dcast(p5$data, substitution + context ~ variable, value.var = "value")
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164 new_sig_matrix = format(new_sig_matrix, scientific=TRUE)
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165 write.table(new_sig_matrix, file=opt$sigmatrix, quote = FALSE, row.names = FALSE, sep="\t")
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166 grid.arrange(p5)
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167 # Visualize the contribution of the signatures in a barplot
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168 pc1 <- plot_contribution(nmf_res$contribution, nmf_res$signature, mode="relative", coord_flip = TRUE)
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169 # Visualize the contribution of the signatures in absolute number of mutations
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170 pc2 <- plot_contribution(nmf_res$contribution, nmf_res$signature, mode="absolute", coord_flip = TRUE)
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171 # Combine the two plots:
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172 grid.arrange(pc1, pc2)
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173
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174 # The relative contribution of each signature for each sample can also be plotted as a heatmap with
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175 # plot_contribution_heatmap, which might be easier to interpret and compare than stacked barplots.
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176 # The samples can be hierarchically clustered based on their euclidean dis- tance. The signatures
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177 # can be plotted in a user-specified order.
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178 # Plot signature contribution as a heatmap with sample clustering dendrogram and a specified signature order:
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179 pch1 <- plot_contribution_heatmap(nmf_res$contribution,
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180 sig_order = paste0("NewSig_", 1:opt$newsignum))
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181 # Plot signature contribution as a heatmap without sample clustering:
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182 pch2 <- plot_contribution_heatmap(nmf_res$contribution, cluster_samples=FALSE)
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183 #Combine the plots into one figure:
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184 grid.arrange(pch1, pch2, ncol = 2, widths = c(2,1.6))
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185
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186 # Compare the reconstructed mutational profile with the original mutational profile:
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187 plot_compare_profiles(pseudo_mut_mat[,1],
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188 nmf_res$reconstructed[,1],
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189 profile_names = c("Original", "Reconstructed"),
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190 condensed = TRUE)
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191 dev.off()
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192 }
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193 ##### Section 3: Find optimal contribution of known signatures: COSMIC mutational signatures ####
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194
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195 if (!is.na(opt$output_cosmic)[1]) {
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196 pdf(opt$output_cosmic, paper = "special", width = 11.69, height = 11.69)
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197 pseudo_mut_mat <- mut_mat + 0.0001 # First add a small psuedocount to the mutation count matrix
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198 if (opt$cosmic_version == "v2") {
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199 sp_url <- paste("https://cancer.sanger.ac.uk/cancergenome/assets/", "signatures_probabilities.txt", sep = "")
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200 cancer_signatures = read.table(sp_url, sep = "\t", header = TRUE)
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201 new_order = match(row.names(pseudo_mut_mat), cancer_signatures$Somatic.Mutation.Type)
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202 cancer_signatures = cancer_signatures[as.vector(new_order),]
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203 row.names(cancer_signatures) = cancer_signatures$Somatic.Mutation.Type
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204 cancer_signatures = as.matrix(cancer_signatures[,4:33])
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205 colnames(cancer_signatures) <- gsub("Signature.", "", colnames(cancer_signatures)) # shorten signature labels
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206 cosmic_tag <- "Signatures (Cosmic v2, March 2015)"
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207 } else {
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208 sp_url <- "https://raw.githubusercontent.com/ARTbio/startbio/master/sigProfiler_SBS_signatures_2019_05_22.tsv"
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209 cancer_signatures = read.table(sp_url, sep = "\t", header = TRUE)
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210 new_order = match(row.names(pseudo_mut_mat), cancer_signatures$Somatic.Mutation.Type)
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211 cancer_signatures = cancer_signatures[as.vector(new_order),]
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212 row.names(cancer_signatures) = cancer_signatures$Somatic.Mutation.Type
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213 cancer_signatures = as.matrix(cancer_signatures[,4:70])
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214 colnames(cancer_signatures) <- gsub("SBS", "", colnames(cancer_signatures)) # shorten signature labels
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215 cosmic_tag <- "Signatures (Cosmic v3, May 2019)"
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216 }
2
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217
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218 # Plot mutational profiles of the COSMIC signatures
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219 if (opt$cosmic_version == "v2") {
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220 p6 <- plot_96_profile(cancer_signatures, condensed = TRUE, ymax = 0.3)
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221 grid.arrange(p6, top = textGrob("COSMIC signature profiles",gp=gpar(fontsize=12,font=3)))
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222 } else {
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223 print(length(cancer_signatures))
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224 p6 <- plot_96_profile(cancer_signatures[,1:33], condensed = TRUE, ymax = 0.3)
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225 p6bis <- plot_96_profile(cancer_signatures[,34:67], condensed = TRUE, ymax = 0.3)
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226 grid.arrange(p6, top = textGrob("COSMIC signature profiles (on two pages)",gp=gpar(fontsize=12,font=3)))
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227 grid.arrange(p6bis, top = textGrob("COSMIC signature profiles (continued)",gp=gpar(fontsize=12,font=3)))
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228 }
2
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229
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230 # Hierarchically cluster the COSMIC signatures based on their similarity with average linkage
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231 # hclust_cosmic = cluster_signatures(cancer_signatures, method = "average")
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232 # store signatures in new order
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233 # cosmic_order = colnames(cancer_signatures)[hclust_cosmic$order]
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234 # plot(hclust_cosmic)
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235
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236 # Similarity between mutational profiles and COSMIC signatures
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237
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238
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239 # The similarity between each mutational profile and each COSMIC signature, can be calculated
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240 # with cos_sim_matrix, and visualized with plot_cosine_heatmap. The cosine similarity reflects
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241 # how well each mutational profile can be explained by each signature individually. The advantage
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242 # of this heatmap representation is that it shows in a glance the similarity in mutational
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243 # profiles between samples, while at the same time providing information on which signatures
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244 # are most prominent. The samples can be hierarchically clustered in plot_cosine_heatmap.
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245 # The cosine similarity between two mutational profiles/signatures can be calculated with cos_sim :
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246 # cos_sim(mut_mat[,1], cancer_signatures[,1])
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247
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248 # Calculate pairwise cosine similarity between mutational profiles and COSMIC signatures
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249
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250 # cos_sim_samples_signatures = cos_sim_matrix(mut_mat, cancer_signatures)
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251 # Plot heatmap with specified signature order
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252 # p.trans <- plot_cosine_heatmap(cos_sim_samples_signatures, col_order = cosmic_order, cluster_rows = TRUE)
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253 # grid.arrange(p.trans)
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254
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255 # Find optimal contribution of COSMIC signatures to reconstruct 96 mutational profiles
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256 fit_res <- fit_to_signatures(pseudo_mut_mat, cancer_signatures)
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257
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258 # Select signatures with some contribution (above a threshold)
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259 threshold <- tail(sort(unlist(rowSums(fit_res$contribution), use.names = FALSE)), opt$signum)[1]
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260 select <- which(rowSums(fit_res$contribution) >= threshold) # ensure opt$signum best signatures in samples are retained, the others discarded
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261 # Plot contribution barplots
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262 pc3 <- plot_contribution(fit_res$contribution[select,], cancer_signatures[,select], coord_flip = T, mode = "absolute")
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263 pc4 <- plot_contribution(fit_res$contribution[select,], cancer_signatures[,select], coord_flip = T, mode = "relative")
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264 #####
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265 # ggplot2 alternative
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266 if (!is.na(opt$levels)[1]) { # if there are levels to display in graphs
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267 pc3_data <- pc3$data
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268 pc3_data <- merge (pc3_data, metadata_table[,c(1,3)], by.x="Sample", by.y="element_identifier")
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269 pc3 <- ggplot(pc3_data, aes(x=Sample, y=Contribution, fill=as.factor(Signature))) +
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270 geom_bar(stat="identity", position='stack') +
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271 scale_fill_discrete(name="Cosmic\nSignature") +
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272 labs(x = "Samples", y = "Absolute contribution") + theme_bw() +
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273 theme(panel.grid.minor.x = element_blank(), panel.grid.major.x = element_blank()) +
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274 facet_grid(~level, scales = "free_x")
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275 pc4_data <- pc4$data
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276 pc4_data <- merge (pc4_data, metadata_table[,c(1,3)], by.x="Sample", by.y="element_identifier")
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277 pc4 <- ggplot(pc4_data, aes(x=Sample, y=Contribution, fill=as.factor(Signature))) +
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278 geom_bar(stat="identity", position='fill') +
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279 scale_fill_discrete(name="Cosmic\nSignature") +
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280 scale_y_continuous(labels = scales::percent_format(accuracy = 1)) +
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281 labs(x = "Samples", y = "Relative contribution") + theme_bw() +
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282 theme(panel.grid.minor.x = element_blank(), panel.grid.major.x = element_blank()) +
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283 facet_grid(~level, scales = "free_x")
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284 }
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285 # Combine the two plots:
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286 grid.arrange(pc3, pc4, top = textGrob("Absolute and Relative Contributions of Cosmic signatures to mutational patterns",gp=gpar(fontsize=12,font=3)))
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287 ## pie charts of comic signatures contributions in samples
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288
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289 sig_data_pie <- as.data.frame(t(head(fit_res$contribution[select,])))
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290 colnames(sig_data_pie) <- gsub("nature", "", colnames(sig_data_pie))
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291 sig_data_pie_percents <- sig_data_pie / (apply(sig_data_pie,1,sum)) * 100
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292 sig_data_pie_percents$sample <- rownames(sig_data_pie_percents)
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293 library(reshape2)
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294 melted_sig_data_pie_percents <-melt(data=sig_data_pie_percents)
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295 melted_sig_data_pie_percents$label <- sub("Sig.", "", melted_sig_data_pie_percents$variable)
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296 melted_sig_data_pie_percents$pos <- cumsum(melted_sig_data_pie_percents$value) - melted_sig_data_pie_percents$value/2
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297 p7 <- ggplot(melted_sig_data_pie_percents, aes(x="", y=value, group=variable, fill=variable)) +
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298 geom_bar(width = 1, stat = "identity") +
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299 geom_text(aes(label = label), position = position_stack(vjust = 0.5), color="black", size=3) +
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300 coord_polar("y", start=0) + facet_wrap(~ sample) +
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301 labs(x="", y="Samples", fill = cosmic_tag) +
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302 theme(axis.text = element_blank(),
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303 axis.ticks = element_blank(),
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304 panel.grid = element_blank())
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305 grid.arrange(p7)
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306
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307 # Plot relative contribution of the cancer signatures in each sample as a heatmap with sample clustering
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308 p8 <- plot_contribution_heatmap(fit_res$contribution, cluster_samples = TRUE, method = "complete")
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309 grid.arrange(p8)
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310
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311 # Compare the reconstructed mutational profile of sample 1 with its original mutational profile
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312 # plot_compare_profiles(mut_mat[,1], fit_res$reconstructed[,1],
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313 # profile_names = c("Original", "Reconstructed"),
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314 # condensed = TRUE)
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315
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316 # Calculate the cosine similarity between all original and reconstructed mutational profiles with
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317 # `cos_sim_matrix`
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318
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319 # calculate all pairwise cosine similarities
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320 cos_sim_ori_rec <- cos_sim_matrix(pseudo_mut_mat, fit_res$reconstructed)
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321 # extract cosine similarities per sample between original and reconstructed
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322 cos_sim_ori_rec <- as.data.frame(diag(cos_sim_ori_rec))
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323
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324 # We can use ggplot to make a barplot of the cosine similarities between the original and
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325 # reconstructed mutational profile of each sample. This clearly shows how well each mutational
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326 # profile can be reconstructed with the COSMIC mutational signatures. Two identical profiles
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327 # have a cosine similarity of 1. The lower the cosine similarity between original and
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328 # reconstructed, the less well the original mutational profile can be reconstructed with
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329 # the COSMIC signatures. You could use, for example, cosine similarity of 0.95 as a cutoff.
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330
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331 # Adjust data frame for plotting with gpplot
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332 colnames(cos_sim_ori_rec) = "cos_sim"
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333 cos_sim_ori_rec$sample = row.names(cos_sim_ori_rec)
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334 # Make barplot
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335 p9 <- ggplot(cos_sim_ori_rec, aes(y=cos_sim, x=sample)) +
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336 geom_bar(stat="identity", fill = "skyblue4") +
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337 coord_cartesian(ylim=c(0.8, 1)) +
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338 # coord_flip(ylim=c(0.8,1)) +
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339 ylab("Cosine similarity\n original VS reconstructed") +
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340 xlab("") +
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341 # 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"
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342 # xlim(rev(levels(factor(cos_sim_ori_rec$sample)))) +
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343 theme_bw() +
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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344 theme(panel.grid.minor.y=element_blank(),
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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345 panel.grid.major.y=element_blank()) +
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346 # Add cut.off line
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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347 geom_hline(aes(yintercept=.95))
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348 grid.arrange(p9, top = textGrob("Similarity between true and reconstructed profiles (with all Cosmic sig.)",gp=gpar(fontsize=12,font=3)))
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349 dev.off()
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350 }
3
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351
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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352
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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353 # Output RData file
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354 if (!is.null(opt$rdata)) {
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355 save.image(file=opt$rdata)
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356 }