Mercurial > repos > artbio > mutational_patterns
annotate mutational_patterns.R @ 16:31e7a33ecd71 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 9deb533aabc9dc24bb88b98c57e242785142df75"
author | artbio |
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date | Mon, 04 Oct 2021 00:35:06 +0000 |
parents | 8182d1625433 |
children | 8c6ee1c2248f |
rev | line source |
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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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1 # load packages that are provided in the conda env |
14
56c8869a231e
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
artbio
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2 options(show.error.messages = F, |
56c8869a231e
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
artbio
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3 error = function() { |
56c8869a231e
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
artbio
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4 cat(geterrmessage(), file = stderr()); q("no", 1, F) |
56c8869a231e
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
artbio
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5 } |
56c8869a231e
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
artbio
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6 ) |
0
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
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7 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
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8 warnings() |
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
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9 library(optparse) |
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
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10 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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0
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11 library(grid) |
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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12 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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13 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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14 library(RColorBrewer) |
0
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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15 |
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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16 # Arguments |
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56c8869a231e
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
artbio
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17 option_list <- list( |
0
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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18 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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19 "--inputs", |
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
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20 default = NA, |
14
56c8869a231e
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
artbio
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21 type = "character", |
0
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
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22 help = "json formatted dictionary of datasets and their paths" |
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
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23 ), |
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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24 make_option( |
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
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25 "--genome", |
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
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26 default = NA, |
14
56c8869a231e
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
artbio
parents:
13
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27 type = "character", |
0
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff
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28 help = "genome name in the BSgenome bioconductor package" |
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff
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29 ), |
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
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30 make_option( |
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
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31 "--levels", |
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
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32 default = NA, |
14
56c8869a231e
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
artbio
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33 type = "character", |
0
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
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34 help = "path to the tab separated file describing the levels in function of datasets" |
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
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35 ), |
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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36 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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2
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37 "--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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38 default = "v2", |
14
56c8869a231e
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
artbio
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39 type = "character", |
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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40 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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2
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41 ), |
e332cf9dfa06
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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2
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42 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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43 "--signum", |
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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44 default = 2, |
14
56c8869a231e
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
artbio
parents:
13
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45 type = "integer", |
0
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff
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46 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
parents:
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47 ), |
924c527fb379
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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48 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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0
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49 "--nrun", |
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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50 default = 2, |
14
56c8869a231e
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
artbio
parents:
13
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51 type = "integer", |
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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52 help = "Number of runs to fit signatures" |
aea952be68cb
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents:
0
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53 ), |
aea952be68cb
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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0
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54 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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55 "--rank", |
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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56 default = 2, |
14
56c8869a231e
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
artbio
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13
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57 type = "integer", |
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 help = "number of ranks to display for parameter optimization" |
aea952be68cb
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents:
0
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59 ), |
aea952be68cb
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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60 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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0
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61 "--newsignum", |
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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62 default = 2, |
14
56c8869a231e
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
artbio
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13
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63 type = "integer", |
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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64 help = "Number of new signatures to be captured" |
aea952be68cb
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents:
0
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65 ), |
aea952be68cb
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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0
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66 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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0
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67 "--output_spectrum", |
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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68 default = NA, |
14
56c8869a231e
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
artbio
parents:
13
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69 type = "character", |
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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70 help = "path to output dataset" |
aea952be68cb
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents:
0
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71 ), |
aea952be68cb
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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0
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72 make_option( |
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 "--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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74 default = NA, |
14
56c8869a231e
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
artbio
parents:
13
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75 type = "character", |
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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76 help = "path to output dataset" |
aea952be68cb
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents:
0
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77 ), |
aea952be68cb
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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0
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78 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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2
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79 "--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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80 default = NA, |
14
56c8869a231e
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
artbio
parents:
13
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81 type = "character", |
3
e332cf9dfa06
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents:
2
diff
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82 help = "path to signature matrix" |
e332cf9dfa06
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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83 ), |
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84 make_option( |
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85 "--output_cosmic", |
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86 default = NA, |
14
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87 type = "character", |
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88 help = "path to output dataset" |
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89 ), |
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90 make_option( |
11
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91 "--sig_contrib_matrix", |
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92 default = NA, |
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93 type = "character", |
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94 help = "path to signature contribution matrix" |
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95 ), |
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96 make_option( |
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97 c("-r", "--rdata"), |
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98 type = "character", |
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99 default = NULL, |
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100 help = "Path to RData output file") |
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101 ) |
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102 |
14
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103 opt <- parse_args(OptionParser(option_list = option_list), |
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104 args = commandArgs(trailingOnly = TRUE)) |
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105 |
2
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106 ################ Manage input data #################### |
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107 json_dict <- opt$inputs |
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108 parser <- newJSONParser() |
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109 parser$addData(json_dict) |
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110 fileslist <- parser$getObject() |
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111 vcf_paths <- attr(fileslist, "names") |
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112 element_identifiers <- unname(unlist(fileslist)) |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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113 ref_genome <- opt$genome |
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114 vcf_table <- data.frame(element_identifier = as.character(element_identifiers), path = vcf_paths) |
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115 |
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116 library(MutationalPatterns) |
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117 library(ref_genome, character.only = TRUE) |
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118 library(ggplot2) |
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119 |
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120 # Load the VCF files into a GRangesList: |
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121 vcfs <- read_vcfs_as_granges(vcf_paths, element_identifiers, ref_genome) |
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122 library(plyr) |
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123 if (!is.na(opt$levels)[1]) { # manage levels if there are |
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124 levels_table <- read.delim(opt$levels, header = FALSE, |
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125 col.names = c("element_identifier", "level")) |
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126 } else { |
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127 levels_table <- data.frame(element_identifier = vcf_table$element_identifier, |
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128 level = rep("nolabels", length(vcf_table$element_identifier))) |
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129 } |
8
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130 metadata_table <- join(vcf_table, levels_table, by = "element_identifier") |
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131 tissue <- as.vector(metadata_table$level) |
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132 detach(package:plyr) |
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133 |
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134 ##### This is done for any section ###### |
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135 mut_mat <- mut_matrix(vcf_list = vcfs, ref_genome = ref_genome) |
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136 qual_col_pals <- brewer.pal.info[brewer.pal.info$category == "qual", ] |
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137 col_vector <- unique(unlist(mapply(brewer.pal, qual_col_pals$maxcolors, rownames(qual_col_pals)))) |
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138 col_vector <- col_vector[c(-32, -34, -39)] # 67-color palette |
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139 |
2
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140 ###### Section 1 Mutation characteristics and spectrums ############# |
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141 if (!is.na(opt$output_spectrum)[1]) { |
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142 pdf(opt$output_spectrum, paper = "special", width = 11.69, height = 11.69) |
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143 type_occurrences <- mut_type_occurrences(vcfs, ref_genome) |
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144 |
2
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145 # mutation spectrum, total or by sample |
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146 |
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147 if (length(levels(factor(levels_table$level))) == 1) { |
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148 p1 <- plot_spectrum(type_occurrences, CT = TRUE, legend = TRUE) |
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149 plot(p1) |
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150 } else { |
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151 p2 <- plot_spectrum(type_occurrences, by = tissue, CT = TRUE) # by levels |
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152 p3 <- plot_spectrum(type_occurrences, CT = TRUE, legend = TRUE) # total |
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153 grid.arrange(p2, p3, ncol = 2, widths = c(4, 2.3), heights = c(4, 1)) |
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154 } |
2
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155 plot_96_profile(mut_mat, condensed = TRUE) |
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156 dev.off() |
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157 } |
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158 |
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159 ###### Section 2: De novo mutational signature extraction using NMF ####### |
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160 # opt$rank cannot be higher than the number of samples and |
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161 # likewise, opt$signum cannot be higher thant the number of samples |
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162 if (!is.na(opt$output_denovo)[1]) { |
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163 |
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164 if (opt$rank > length(element_identifiers)) { |
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165 opt$rank <- length(element_identifiers) |
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166 } |
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167 if (opt$signum > length(element_identifiers)) { |
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168 opt$signum <- length(element_identifiers) |
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169 } |
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170 pseudo_mut_mat <- mut_mat + 0.0001 # First add a small pseudocount to the mutation count matrix |
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171 # Use the NMF package to generate an estimate rank plot |
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172 library("NMF") |
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173 estimate <- nmf(pseudo_mut_mat, rank = 1:opt$rank, method = "brunet", nrun = opt$nrun, seed = 123456) |
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174 # And plot it |
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175 pdf(opt$output_denovo, paper = "special", width = 11.69, height = 11.69) |
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176 p4 <- plot(estimate) |
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177 grid.arrange(p4) |
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178 # Extract 4 (PARAMETIZE) mutational signatures from the mutation count matrix with extract_signatures |
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179 # (For larger datasets it is wise to perform more iterations by changing the nrun parameter |
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180 # to achieve stability and avoid local minima) |
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181 nmf_res <- extract_signatures(pseudo_mut_mat, rank = opt$newsignum, nrun = opt$nrun) |
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182 # Assign signature names |
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183 colnames(nmf_res$signatures) <- paste0("NewSig_", 1:opt$newsignum) |
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184 rownames(nmf_res$contribution) <- paste0("NewSig_", 1:opt$newsignum) |
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185 # Plot the 96-profile of the signatures: |
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186 p5 <- plot_96_profile(nmf_res$signatures, condensed = TRUE) |
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187 new_sig_matrix <- reshape2::dcast(p5$data, substitution + context ~ sample, value.var = "freq") |
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188 new_sig_matrix <- format(new_sig_matrix, scientific = TRUE) |
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189 write.table(new_sig_matrix, file = opt$sigmatrix, quote = FALSE, row.names = FALSE, sep = "\t") |
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190 grid.arrange(p5) |
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191 # Visualize the contribution of the signatures in a barplot |
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192 pc1 <- plot_contribution(nmf_res$contribution, nmf_res$signature, mode = "relative", coord_flip = TRUE) |
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193 # Visualize the contribution of the signatures in absolute number of mutations |
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194 pc2 <- plot_contribution(nmf_res$contribution, nmf_res$signature, mode = "absolute", coord_flip = TRUE) |
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195 # Combine the two plots: |
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196 grid.arrange(pc1, pc2) |
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197 |
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198 # The relative contribution of each signature for each sample can also be plotted as a heatmap with |
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199 # plot_contribution_heatmap, which might be easier to interpret and compare than stacked barplots. |
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200 # The samples can be hierarchically clustered based on their euclidean dis- tance. The signatures |
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201 # can be plotted in a user-specified order. |
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202 # Plot signature contribution as a heatmap with sample clustering dendrogram and a specified signature order: |
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203 pch1 <- plot_contribution_heatmap(nmf_res$contribution, |
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204 sig_order = paste0("NewSig_", 1:opt$newsignum)) |
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205 # Plot signature contribution as a heatmap without sample clustering: |
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206 pch2 <- plot_contribution_heatmap(nmf_res$contribution, cluster_samples = FALSE) |
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207 #Combine the plots into one figure: |
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208 grid.arrange(pch1, pch2, ncol = 2, widths = c(2, 1.6)) |
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209 |
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210 # Compare the reconstructed mutational profile with the original mutational profile: |
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211 plot_compare_profiles(pseudo_mut_mat[, 1], |
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212 nmf_res$reconstructed[, 1], |
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213 profile_names = c("Original", "Reconstructed"), |
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214 condensed = TRUE) |
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215 dev.off() |
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216 } |
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217 ##### Section 3: Find optimal contribution of known signatures: COSMIC mutational signatures #### |
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218 |
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219 if (!is.na(opt$output_cosmic)[1]) { |
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220 pdf(opt$output_cosmic, paper = "special", width = 11.69, height = 11.69) |
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221 pseudo_mut_mat <- mut_mat + 0.0001 # First add a small psuedocount to the mutation count matrix |
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222 if (opt$cosmic_version == "v2") { |
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223 sp_url <- "https://cancer.sanger.ac.uk/signatures/documents/420/COSMIC_v2_SBS_GRCh38.txt" |
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224 cancer_signatures <- read.table(sp_url, sep = "\t", header = TRUE) |
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225 new_order <- match(row.names(pseudo_mut_mat), cancer_signatures$Type) |
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226 cancer_signatures <- cancer_signatures[as.vector(new_order), ] |
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227 row.names(cancer_signatures) <- cancer_signatures$Type |
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228 cancer_signatures <- as.matrix(cancer_signatures[, 2:31]) |
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229 colnames(cancer_signatures) <- gsub("Signature_", "", colnames(cancer_signatures)) # shorten signature labels |
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230 cosmic_tag <- "Signatures (Cosmic v2, March 2015)" |
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231 cosmic_colors <- col_vector[1:30] |
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232 names(cosmic_colors) <- colnames(cancer_signatures) |
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233 } else { |
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234 sp_url <- "https://cancer.sanger.ac.uk/signatures/documents/431/COSMIC_v3_SBS_GRCh38.txt" |
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235 cancer_signatures <- read.table(sp_url, sep = "\t", header = TRUE) |
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236 new_order <- match(row.names(pseudo_mut_mat), cancer_signatures$Type) |
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237 cancer_signatures <- cancer_signatures[as.vector(new_order), ] |
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238 row.names(cancer_signatures) <- cancer_signatures$Type |
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239 cancer_signatures <- as.matrix(cancer_signatures[, 2:68]) |
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240 colnames(cancer_signatures) <- gsub("SBS", "", colnames(cancer_signatures)) # shorten signature labels |
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241 cosmic_tag <- "Signatures (Cosmic v3, May 2019)" |
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242 cosmic_colors <- col_vector[1:67] |
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243 names(cosmic_colors) <- colnames(cancer_signatures) |
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244 } |
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245 |
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246 # Plot mutational profiles of the COSMIC signatures |
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247 if (opt$cosmic_version == "v2") { |
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248 p6 <- plot_96_profile(cancer_signatures, condensed = TRUE, ymax = 0.3) |
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249 grid.arrange(p6, top = textGrob("COSMIC signature profiles", gp = gpar(fontsize = 12, font = 3))) |
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250 } else { |
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251 p6 <- plot_96_profile(cancer_signatures[, 1:33], condensed = TRUE, ymax = 0.3) |
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252 p6bis <- plot_96_profile(cancer_signatures[, 34:67], condensed = TRUE, ymax = 0.3) |
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253 grid.arrange(p6, top = textGrob("COSMIC signature profiles (on two pages)", |
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254 gp = gpar(fontsize = 12, font = 3))) |
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255 grid.arrange(p6bis, top = textGrob("COSMIC signature profiles (continued)", |
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256 gp = gpar(fontsize = 12, font = 3))) |
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257 } |
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258 |
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259 |
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260 # Find optimal contribution of COSMIC signatures to reconstruct 96 mutational profiles |
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261 fit_res <- fit_to_signatures(pseudo_mut_mat, cancer_signatures) |
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262 |
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263 # Plot contribution barplots |
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264 pc3 <- plot_contribution(fit_res$contribution, cancer_signatures, coord_flip = T, mode = "absolute") |
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265 pc4 <- plot_contribution(fit_res$contribution, cancer_signatures, coord_flip = T, mode = "relative") |
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266 if (is.na(opt$levels)[1]) { # if there are NO levels to display in graphs |
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267 pc3_data <- pc3$data |
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268 pc3 <- ggplot(pc3_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) + |
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269 geom_bar(stat = "identity", position = "stack") + |
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270 coord_flip() + |
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271 scale_fill_manual(name = "Cosmic\nSignatures", values = cosmic_colors) + |
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272 labs(x = "Samples", y = "Absolute contribution") + theme_bw() + |
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273 theme(panel.grid.minor.x = element_blank(), |
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274 panel.grid.major.x = element_blank(), |
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275 legend.position = "right", |
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276 text = element_text(size = 8), |
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277 axis.text.x = element_text(angle = 90, hjust = 1)) |
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278 pc4_data <- pc4$data |
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279 pc4 <- ggplot(pc4_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) + |
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280 geom_bar(stat = "identity", position = "fill") + |
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281 coord_flip() + |
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282 scale_fill_manual(name = "Cosmic\nSignatures", values = cosmic_colors) + |
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283 scale_y_continuous(labels = scales::percent_format(accuracy = 1)) + |
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284 labs(x = "Samples", y = "Relative contribution") + theme_bw() + |
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285 theme(panel.grid.minor.x = element_blank(), panel.grid.major.x = element_blank(), legend.position = "right", |
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286 text = element_text(size = 8), |
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287 axis.text.x = element_text(angle = 90, hjust = 1)) |
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288 } |
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289 ##### |
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290 # ggplot2 alternative |
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291 if (!is.na(opt$levels)[1]) { # if there are levels to display in graphs |
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292 pc3_data <- pc3$data |
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293 pc3_data <- merge(pc3_data, metadata_table[, c(1, 3)], by.x = "Sample", by.y = "element_identifier") |
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294 pc3 <- ggplot(pc3_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) + |
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295 geom_bar(stat = "identity", position = "stack") + |
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296 scale_fill_manual(name = "Cosmic\nSignatures", values = cosmic_colors) + |
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297 labs(x = "Samples", y = "Absolute contribution") + theme_bw() + |
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298 theme(panel.grid.minor.x = element_blank(), |
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299 panel.grid.major.x = element_blank(), |
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300 legend.position = "right", |
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301 text = element_text(size = 8), |
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302 axis.text.x = element_text(angle = 90, hjust = 1)) + |
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303 facet_grid(~level, scales = "free_x", space = "free") |
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304 pc4_data <- pc4$data |
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305 pc4_data <- merge(pc4_data, metadata_table[, c(1, 3)], by.x = "Sample", by.y = "element_identifier") |
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306 pc4 <- ggplot(pc4_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) + |
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307 geom_bar(stat = "identity", position = "fill") + |
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308 scale_fill_manual(name = "Cosmic\nSignatures", values = cosmic_colors) + |
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309 scale_y_continuous(labels = scales::percent_format(accuracy = 1)) + |
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310 labs(x = "Samples", y = "Relative contribution") + theme_bw() + |
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311 theme(panel.grid.minor.x = element_blank(), |
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312 panel.grid.major.x = element_blank(), |
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313 legend.position = "right", |
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314 text = element_text(size = 8), |
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315 axis.text.x = element_text(angle = 90, hjust = 1)) + |
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316 facet_grid(~level, scales = "free_x", space = "free") |
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317 } |
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318 # Combine the two plots: |
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319 grid.arrange(pc3, pc4, |
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320 top = textGrob("Absolute and Relative Contributions of Cosmic signatures to mutational patterns", |
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321 gp = gpar(fontsize = 12, font = 3))) |
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322 |
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323 #### pie charts of comic signatures contributions in samples ### |
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324 library(reshape2) |
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325 library(dplyr) |
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326 if (length(levels(factor(levels_table$level))) < 2) { |
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327 fit_res_contrib <- as.data.frame(fit_res$contribution) |
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328 worklist <- cbind(signature = rownames(fit_res$contribution), |
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329 level = rep("nolabels", length(fit_res_contrib[, 1])), |
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330 fit_res_contrib, |
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331 sum = rowSums(fit_res_contrib)) |
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332 worklist <- worklist[order(worklist[, "sum"], decreasing = T), ] |
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333 worklist <- worklist[1:opt$signum, ] |
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334 worklist <- worklist[, -length(worklist[1, ])] |
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335 worklist <- melt(worklist) |
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336 worklist <- worklist[, c(1, 3, 4, 2)] |
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337 } else { |
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338 worklist <- list() |
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339 for (i in levels(factor(levels_table$level))) { |
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340 fit_res$contribution[, levels_table$element_identifier[levels_table$level == i]] -> worklist[[i]] |
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341 sum <- rowSums(as.data.frame(worklist[[i]])) |
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342 worklist[[i]] <- cbind(worklist[[i]], sum) |
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343 worklist[[i]] <- worklist[[i]][order(worklist[[i]][, "sum"], decreasing = T), ] |
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344 worklist[[i]] <- worklist[[i]][1:opt$signum, ] |
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345 worklist[[i]] <- worklist[[i]][, -length(as.data.frame(worklist[[i]]))] |
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346 } |
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347 worklist <- as.data.frame(melt(worklist)) |
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348 worklist[, 2] <- paste0(worklist[, 4], " - ", worklist[, 2]) |
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349 } |
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350 |
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351 colnames(worklist) <- c("signature", "sample", "value", "level") |
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352 worklist <- as.data.frame(worklist %>% group_by(sample) %>% mutate(value = value / sum(value) * 100)) |
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353 worklist$pos <- cumsum(worklist$value) - worklist$value / 2 |
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354 worklist$label <- factor(worklist$signature) |
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355 worklist$signature <- factor(worklist$signature) |
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356 p7 <- ggplot(worklist, aes(x = "", y = value, group = signature, fill = signature)) + |
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357 geom_bar(width = 1, stat = "identity") + |
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358 geom_text(aes(label = label), position = position_stack(vjust = 0.5), color = "black", size = 3) + |
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359 coord_polar("y", start = 0) + facet_wrap(.~sample) + |
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360 labs(x = "", y = "Samples", fill = cosmic_tag) + |
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361 scale_fill_manual(name = paste0(opt$signum, " most contributing\nsignatures\n(in each label/tissue)"), |
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362 values = cosmic_colors[levels(worklist$signature)]) + |
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363 theme(axis.text = element_blank(), |
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364 axis.ticks = element_blank(), |
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365 panel.grid = element_blank()) |
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366 grid.arrange(p7) |
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367 |
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368 # Plot relative contribution of the cancer signatures in each sample as a heatmap with sample clustering |
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369 if (length(vcf_paths) > 1) { |
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370 p8 <- plot_contribution_heatmap(fit_res$contribution, cluster_samples = TRUE, method = "complete") |
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371 grid.arrange(p8) |
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372 } |
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373 |
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374 # export relative contribution matrix |
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375 if (!is.na(opt$sig_contrib_matrix)) { |
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376 output_table <- t(fit_res$contribution) / rowSums(t(fit_res$contribution)) |
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377 colnames(output_table) <- paste0("s", colnames(output_table)) |
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378 if (length(levels(factor(levels_table$level))) > 1) { |
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379 output_table <- data.frame(sample = paste0(metadata_table[metadata_table$element_identifier == colnames(fit_res$contribution), |
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380 3], "-", colnames(fit_res$contribution)), |
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381 output_table) |
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382 } else { |
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383 output_table <- data.frame(sample = rownames(output_table), output_table) |
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384 } |
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385 write.table(output_table, file = opt$sig_contrib_matrix, sep = "\t", quote = F, row.names = F) |
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386 } |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460"
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387 |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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388 # calculate all pairwise cosine similarities |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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389 cos_sim_ori_rec <- cos_sim_matrix(pseudo_mut_mat, fit_res$reconstructed) |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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390 # extract cosine similarities per sample between original and reconstructed |
aea952be68cb
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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391 cos_sim_ori_rec <- as.data.frame(diag(cos_sim_ori_rec)) |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
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392 |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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393 # We can use ggplot to make a barplot of the cosine similarities between the original and |
aea952be68cb
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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394 # reconstructed mutational profile of each sample. This clearly shows how well each mutational |
aea952be68cb
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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395 # profile can be reconstructed with the COSMIC mutational signatures. Two identical profiles |
aea952be68cb
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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396 # have a cosine similarity of 1. The lower the cosine similarity between original and |
aea952be68cb
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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397 # reconstructed, the less well the original mutational profile can be reconstructed with |
aea952be68cb
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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398 # the COSMIC signatures. You could use, for example, cosine similarity of 0.95 as a cutoff. |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
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399 |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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400 # Adjust data frame for plotting with gpplot |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
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401 colnames(cos_sim_ori_rec) <- "cos_sim" |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
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402 cos_sim_ori_rec$sample <- row.names(cos_sim_ori_rec) |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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403 # Make barplot |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
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404 p9 <- ggplot(cos_sim_ori_rec, aes(y = cos_sim, x = sample)) + |
56c8869a231e
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
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405 geom_bar(stat = "identity", fill = "skyblue4") + |
56c8869a231e
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
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406 coord_cartesian(ylim = c(0.8, 1)) + |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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407 # coord_flip(ylim=c(0.8,1)) + |
aea952be68cb
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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408 ylab("Cosine similarity\n original VS reconstructed") + |
aea952be68cb
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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409 xlab("") + |
aea952be68cb
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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410 # 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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411 # xlim(rev(levels(factor(cos_sim_ori_rec$sample)))) + |
aea952be68cb
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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412 theme_bw() + |
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413 theme(panel.grid.minor.y = element_blank(), |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
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414 panel.grid.major.y = element_blank()) + |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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415 # Add cut.off line |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
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416 geom_hline(aes(yintercept = .95)) |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
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417 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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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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418 dev.off() |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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419 } |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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420 |
e332cf9dfa06
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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421 |
e332cf9dfa06
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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422 # Output RData file |
e332cf9dfa06
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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423 if (!is.null(opt$rdata)) { |
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424 save.image(file = opt$rdata) |
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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425 } |