Mercurial > repos > artbio > mutational_patterns

annotate mutational_patterns.R @ 19:69f09dff98f9 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit db5fd077ec6c840b7b6eda331820999f85fd7c26"
author artbio
date Sun, 17 Oct 2021 23:05:01 +0000
parents 8d9f31389f33
children a2cb7dc9250a
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924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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1 # load packages that are provided in the conda env
14
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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"
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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"
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4 cat(geterrmessage(), file = stderr()); q("no", 1, F)
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5 }
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
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6 )
0
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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"
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8 warnings()
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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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"
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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"
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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"
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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"
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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"
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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"
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15
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16 # Arguments
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17 option_list <- list(
0
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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"
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19 "--inputs",
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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20 default = NA,
14
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21 type = "character",
0
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22 help = "json formatted dictionary of datasets and their paths"
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23 ),
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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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"
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25 "--genome",
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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26 default = NA,
14
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artbio
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27 type = "character",
0
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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"
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29 ),
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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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
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31 "--levels",
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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32 default = NA,
14
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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"
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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"
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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"
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37 "--cosmic_version",
18
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38 default = NA,
14
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artbio
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39 type = "character",
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
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40 help = "Version of the Cosmic Signature set to be used to express mutational profiles"
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
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41 ),
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
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42 make_option(
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
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43 "--own_signatures",
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
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44 default = NA,
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
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45 type = "character",
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
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46 help = "Path to the user-defined signature matrix"
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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47 ),
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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48 make_option(
0
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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49 "--signum",
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
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50 default = 2,
14
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artbio
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51 type = "integer",
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
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52 help = "selects the N most significant signatures in samples to express mutational profiles"
0
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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53 ),
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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54 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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55 "--nrun",
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 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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57 type = "integer",
2
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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58 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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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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diff changeset
61 "--rank",
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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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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63 type = "integer",
2
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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64 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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65 ),
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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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
parents: 0
diff changeset
67 "--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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68 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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69 type = "integer",
2
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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70 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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71 ),
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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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
diff changeset
73 "--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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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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diff changeset
78 make_option(
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 0
diff changeset
79 "--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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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",
2
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 0
diff changeset
82 help = "path to output dataset"
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 0
diff changeset
83 ),
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 0
diff changeset
84 make_option(
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
85 "--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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86 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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87 type = "character",
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
88 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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89 ),
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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diff changeset
90 make_option(
18
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91 "--output_sigpattern",
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92 default = NA,
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93 type = "character",
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94 help = "path to output dataset"
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95 ),
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96 make_option(
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97 "--sig_contrib_matrix",
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98 default = NA,
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99 type = "character",
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100 help = "path to signature contribution matrix"
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101 ),
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102 make_option(
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103 c("-r", "--rdata"),
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104 type = "character",
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105 default = NULL,
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106 help = "Path to RData output file"
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107 ),
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108 make_option(
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109 c("-t", "--tooldir"),
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110 type = "character",
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111 default = NULL,
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112 help = "Path to tool directory, where tool data are stored")
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113
0
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114 )
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115
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116 opt <- parse_args(OptionParser(option_list = option_list),
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117 args = commandArgs(trailingOnly = TRUE))
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118
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119 ################ Manage input data ####################
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120 json_dict <- opt$inputs
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121 parser <- newJSONParser()
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122 parser$addData(json_dict)
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123 fileslist <- parser$getObject()
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124 vcf_paths <- attr(fileslist, "names")
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125 element_identifiers <- unname(unlist(fileslist))
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126 ref_genome <- opt$genome
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127 vcf_table <- data.frame(element_identifier = as.character(element_identifiers), path = vcf_paths)
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128
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129 library(MutationalPatterns)
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130 library(ref_genome, character.only = TRUE)
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131 library(ggplot2)
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132
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133 # Load the VCF files into a GRangesList:
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134 vcfs <- read_vcfs_as_granges(vcf_paths, element_identifiers, ref_genome)
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135 library(plyr)
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136 if (!is.na(opt$levels)[1]) { # manage levels if there are
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137 levels_table <- read.delim(opt$levels, header = FALSE,
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138 col.names = c("element_identifier", "level"))
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139 } else {
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140 levels_table <- data.frame(element_identifier = vcf_table$element_identifier,
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141 level = rep("nolabels", length(vcf_table$element_identifier)))
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142 }
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143 metadata_table <- join(vcf_table, levels_table, by = "element_identifier")
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144 tissue <- as.vector(metadata_table$level)
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145 detach(package:plyr)
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146
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147 ##### This is done for any section ######
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148 mut_mat <- mut_matrix(vcf_list = vcfs, ref_genome = ref_genome)
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149 qual_col_pals <- brewer.pal.info[brewer.pal.info$category == "qual", ]
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150
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151 ###### Section 1 Mutation characteristics and spectrums #############
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152 if (!is.na(opt$output_spectrum)[1]) {
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153 pdf(opt$output_spectrum, paper = "special", width = 11.69, height = 11.69)
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154 type_occurrences <- mut_type_occurrences(vcfs, ref_genome)
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155
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156 # mutation spectrum, total or by sample
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157
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158 if (length(levels(factor(levels_table$level))) == 1) {
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159 p1 <- plot_spectrum(type_occurrences, CT = TRUE, legend = TRUE)
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160 plot(p1)
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161 } else {
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162 p2 <- plot_spectrum(type_occurrences, by = tissue, CT = TRUE) # by levels
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163 p3 <- plot_spectrum(type_occurrences, CT = TRUE, legend = TRUE) # total
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164 grid.arrange(p2, p3, ncol = 2, widths = c(4, 2.3), heights = c(4, 1))
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165 }
2
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166 plot_96_profile(mut_mat, condensed = TRUE)
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167 dev.off()
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168 }
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169
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170 ###### Section 2: De novo mutational signature extraction using NMF #######
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171 # opt$rank cannot be higher than the number of samples and
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172 # likewise, opt$signum cannot be higher thant the number of samples
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173 if (!is.na(opt$output_denovo)[1]) {
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174
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175 if (opt$rank > length(element_identifiers)) {
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176 opt$rank <- length(element_identifiers)
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177 }
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178 if (opt$signum > length(element_identifiers)) {
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179 opt$signum <- length(element_identifiers)
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180 }
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181 pseudo_mut_mat <- mut_mat + 0.0001 # First add a small pseudocount to the mutation count matrix
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182 # Use the NMF package to generate an estimate rank plot
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183 library("NMF")
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184 estimate <- nmf(pseudo_mut_mat, rank = 1:opt$rank, method = "brunet", nrun = opt$nrun, seed = 123456)
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185 # And plot it
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186 pdf(opt$output_denovo, paper = "special", width = 11.69, height = 11.69)
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187 p4 <- plot(estimate)
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188 grid.arrange(p4)
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189 # Extract 4 (PARAMETIZE) mutational signatures from the mutation count matrix with extract_signatures
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190 # (For larger datasets it is wise to perform more iterations by changing the nrun parameter
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191 # to achieve stability and avoid local minima)
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192 nmf_res <- extract_signatures(pseudo_mut_mat, rank = opt$newsignum, nrun = opt$nrun)
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193 # Assign signature names
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194 colnames(nmf_res$signatures) <- paste0("NewSig_", 1:opt$newsignum)
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195 rownames(nmf_res$contribution) <- paste0("NewSig_", 1:opt$newsignum)
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196 # Plot the 96-profile of the signatures:
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197 p5 <- plot_96_profile(nmf_res$signatures, condensed = TRUE)
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198 new_sig_matrix <- reshape2::dcast(p5$data, substitution + context ~ sample, value.var = "freq")
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199 new_sig_matrix <- format(new_sig_matrix, scientific = TRUE)
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200 write.table(new_sig_matrix, file = opt$sigmatrix, quote = FALSE, row.names = FALSE, sep = "\t")
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201 grid.arrange(p5)
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202 # Visualize the contribution of the signatures in a barplot
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203 pc1 <- plot_contribution(nmf_res$contribution, nmf_res$signature, mode = "relative", coord_flip = TRUE)
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204 # Visualize the contribution of the signatures in absolute number of mutations
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205 pc2 <- plot_contribution(nmf_res$contribution, nmf_res$signature, mode = "absolute", coord_flip = TRUE)
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206 # Combine the two plots:
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207 grid.arrange(pc1, pc2)
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208
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209 # The relative contribution of each signature for each sample can also be plotted as a heatmap with
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210 # plot_contribution_heatmap, which might be easier to interpret and compare than stacked barplots.
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211 # The samples can be hierarchically clustered based on their euclidean dis- tance. The signatures
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212 # can be plotted in a user-specified order.
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213 # Plot signature contribution as a heatmap with sample clustering dendrogram and a specified signature order:
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214 pch1 <- plot_contribution_heatmap(nmf_res$contribution,
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215 sig_order = paste0("NewSig_", 1:opt$newsignum))
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216 # Plot signature contribution as a heatmap without sample clustering:
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217 pch2 <- plot_contribution_heatmap(nmf_res$contribution, cluster_samples = FALSE)
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218 #Combine the plots into one figure:
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219 grid.arrange(pch1, pch2, ncol = 2, widths = c(2, 1.6))
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220
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221 # Compare the reconstructed mutational profile with the original mutational profile:
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222 plot_compare_profiles(pseudo_mut_mat[, 1],
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223 nmf_res$reconstructed[, 1],
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224 profile_names = c("Original", "Reconstructed"),
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225 condensed = TRUE)
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226 dev.off()
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227 }
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228
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229 ##### Section 3: Find optimal contribution of known signatures: COSMIC or OWN mutational signatures ####
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230
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231 if (!is.na(opt$output_sigpattern)[1]) {
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232 # Prepare cosmic signatures
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233 if (!is.na(opt$cosmic_version)) {
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234 cosmic_urls <- read.delim(paste0(opt$tooldir, "cosmic_urls.tsv"), sep = "\t", header = TRUE)
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235 cosmic_sbs_file <- cosmic_urls$url[cosmic_urls$genome == opt$genome &
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236 cosmic_urls$cosmic_version == opt$cosmic_version]
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237 sbs_signatures <- read.table(paste0(opt$tooldir, cosmic_sbs_file),
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238 sep = "\t", header = TRUE)
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239 tag <- paste(gsub("BSgenome.Hsapiens.UCSC.", "", opt$genome), "COSMIC", opt$cosmic_version, sep = " ")
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240 }
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241 # Prepare user-defined signatures
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242 if (!is.na(opt$own_signatures)) {
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243 sbs_signatures <- read.table(opt$own_signatures, sep = "\t", header = TRUE)
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244 tag <- paste(opt$genome, "User-Defined Signatures", sep = " ")
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245 }
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246 row.names(sbs_signatures) <- sbs_signatures$Type
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247 # drop column Type of sbs_signatures
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248 sbs_signatures <- subset(sbs_signatures, select = -c(Type))
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249 # reorder substitutions of sbs_signatures to match mut_mat
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250 sbs_signatures <- sbs_signatures[match(row.names(mut_mat), row.names(sbs_signatures)), ]
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251 colnames(sbs_signatures) <- gsub("SBS", "", colnames(sbs_signatures))
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252 # arrange signature colors
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253 signature_colors <- c("#3f4100", "#6f53ff", "#6dc400", "#9d1fd7", "#009c06", "#001fae", "#8adb4d", "#5a67ff", "#d8c938", "#024bc3", "#d2ab00",
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254 "#e36eff", "#00ac44", "#d000b0", "#01b071", "#ff64e2", "#006b21", "#b70090", "#60dc9f", "#5f0083", "#c0ce67", "#002981",
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255 "#ffb53e", "#44005f", "#b59600", "#7d95ff", "#f47600", "#017bc4", "#ff2722", "#02cfec", "#ff233f", "#01b7b4", "#fd005c",
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256 "#019560", "#ff57a9", "#88d896", "#b80067", "#abd27f", "#dc8eff", "#667b00", "#fba3ff", "#093f00", "#ff6494", "#009791",
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257 "#c93200", "#4ac8ff", "#a60005", "#8fd4b6", "#ce0036", "#00634d", "#ff6035", "#2d1956", "#f0be6d", "#6a0058", "#957a00",
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258 "#e4b4ff", "#4a5500", "#abc7fe", "#c95900", "#003d27", "#b10043", "#d5c68e", "#3e163e", "#b36b00", "#debaeb", "#605400",
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259 "#7a0044", "#ffa06d", "#4c0d21", "#ff9cb5", "#3f1d02", "#ff958f", "#634a66", "#775500", "#6e0028", "#717653",
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260 "#6c1000", "#693600")
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261 signature_colors <- signature_colors[seq_len(ncol(sbs_signatures))]
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262 names(signature_colors) <- colnames(sbs_signatures)
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263 # To drop signature_colors <- signature_colors[colnames(sbs_signatures)]
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264 # This is IMPORTANT since in Galaxy we do not use the embeded function get_known_signatures()
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265 sbs_signatures <- as.matrix(sbs_signatures)
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266
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267
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268 # Plot mutational profiles of the COSMIC signatures
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269
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270 pdf(opt$output_sigpattern, paper = "special", width = 11.69, height = 11.69)
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271 for (i in head(seq(1, ncol(sbs_signatures), by = 20), -1)) {
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272 p6 <- plot_96_profile(sbs_signatures[, i:(i + 19)], condensed = TRUE, ymax = 0.3)
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273 grid.arrange(p6, top = textGrob(paste0(tag, " profiles (", trunc((i + 1) / 20) + 1, " of ",
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274 trunc(ncol(sbs_signatures) / 20) + 1, " pages)"),
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275 gp = gpar(fontsize = 12, font = 3)))
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276 }
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277 p6 <- plot_96_profile(sbs_signatures[, (trunc(ncol(sbs_signatures) / 20) * 20):(ncol(sbs_signatures))],
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278 condensed = TRUE, ymax = 0.3)
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279 grid.arrange(p6, top = textGrob(paste0(tag, " profiles (", trunc(ncol(sbs_signatures) / 20) + 1, " of ",
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280 trunc(ncol(sbs_signatures) / 20) + 1, " pages)"),
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281 gp = gpar(fontsize = 12, font = 3)))
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282
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283
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284 # Find optimal contribution of COSMIC signatures to reconstruct 96 mutational profiles
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285 pseudo_mut_mat <- mut_mat + 0.0001 # First add a small pseudocount to the mutation count matrix
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286 fit_res <- fit_to_signatures(pseudo_mut_mat, sbs_signatures)
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287
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288 # Plot contribution barplots
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289 pc3 <- plot_contribution(fit_res$contribution, sbs_signatures, coord_flip = T, mode = "absolute")
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290 pc4 <- plot_contribution(fit_res$contribution, sbs_signatures, coord_flip = T, mode = "relative")
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291 if (is.na(opt$levels)[1]) { # if there are NO levels to display in graphs
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292 pc3_data <- pc3$data
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293 pc3 <- ggplot(pc3_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) +
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294 geom_bar(stat = "identity", position = "stack") +
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295 coord_flip() +
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296 scale_fill_manual(name = tag, values = signature_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 pc4_data <- pc4$data
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304 pc4 <- ggplot(pc4_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) +
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305 geom_bar(stat = "identity", position = "fill") +
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306 coord_flip() +
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307 scale_fill_manual(name = tag, values = signature_colors) +
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308 scale_y_continuous(labels = scales::percent_format(accuracy = 1)) +
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309 labs(x = "Samples", y = "Relative contribution") + theme_bw() +
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310 theme(panel.grid.minor.x = element_blank(), panel.grid.major.x = element_blank(), legend.position = "right",
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311 text = element_text(size = 8),
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312 axis.text.x = element_text(angle = 90, hjust = 1))
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313 }
3
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314 #####
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315 # ggplot2 alternative
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316 if (!is.na(opt$levels)[1]) { # if there are levels to display in graphs
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317 pc3_data <- pc3$data
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318 pc3_data <- merge(pc3_data, metadata_table[, c(1, 3)], by.x = "Sample", by.y = "element_identifier")
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319 pc3 <- ggplot(pc3_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) +
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320 geom_bar(stat = "identity", position = "stack") +
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321 scale_fill_manual(name = tag, values = signature_colors) +
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artbio
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322 labs(x = "Samples", y = "Absolute contribution") + theme_bw() +
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323 theme(panel.grid.minor.x = element_blank(),
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324 panel.grid.major.x = element_blank(),
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325 legend.position = "right",
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326 text = element_text(size = 8),
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327 axis.text.x = element_text(angle = 90, hjust = 1)) +
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328 facet_grid(~level, scales = "free_x", space = "free")
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329 pc4_data <- pc4$data
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330 pc4_data <- merge(pc4_data, metadata_table[, c(1, 3)], by.x = "Sample", by.y = "element_identifier")
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331 pc4 <- ggplot(pc4_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) +
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332 geom_bar(stat = "identity", position = "fill") +
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333 scale_fill_manual(name = tag, values = signature_colors) +
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334 scale_y_continuous(labels = scales::percent_format(accuracy = 1)) +
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diff changeset
335 labs(x = "Samples", y = "Relative contribution") + theme_bw() +
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artbio
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diff changeset
336 theme(panel.grid.minor.x = element_blank(),
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artbio
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diff changeset
337 panel.grid.major.x = element_blank(),
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artbio
parents: 13
diff changeset
338 legend.position = "right",
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artbio
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diff changeset
339 text = element_text(size = 8),
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artbio
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diff changeset
340 axis.text.x = element_text(angle = 90, hjust = 1)) +
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artbio
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diff changeset
341 facet_grid(~level, scales = "free_x", space = "free")
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artbio
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diff changeset
342 }
2
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artbio
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diff changeset
343 # Combine the two plots:
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artbio
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diff changeset
344 grid.arrange(pc3, pc4,
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artbio
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diff changeset
345 top = textGrob("Absolute and Relative Contributions of elementary signatures to mutational profiles",
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artbio
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diff changeset
346 gp = gpar(fontsize = 12, font = 3)))
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artbio
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diff changeset
347
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artbio
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diff changeset
348 #### pie charts of comic signatures contributions in samples ###
2
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artbio
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diff changeset
349 library(reshape2)
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artbio
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diff changeset
350 library(dplyr)
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artbio
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diff changeset
351 if (length(levels(factor(levels_table$level))) < 2) {
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artbio
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diff changeset
352 fit_res_contrib <- as.data.frame(fit_res$contribution)
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artbio
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diff changeset
353 worklist <- cbind(signature = rownames(fit_res$contribution),
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artbio
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354 level = rep("nolabels", length(fit_res_contrib[, 1])),
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artbio
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diff changeset
355 fit_res_contrib,
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artbio
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diff changeset
356 sum = rowSums(fit_res_contrib))
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artbio
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diff changeset
357 worklist <- worklist[order(worklist[, "sum"], decreasing = T), ]
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artbio
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diff changeset
358 worklist <- worklist[1:opt$signum, ]
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artbio
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diff changeset
359 worklist <- worklist[, -length(worklist[1, ])]
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artbio
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diff changeset
360 worklist <- melt(worklist)
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artbio
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diff changeset
361 worklist <- worklist[, c(1, 3, 4, 2)]
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e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710"
artbio
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diff changeset
362 } else {
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artbio
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diff changeset
363 worklist <- list()
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artbio
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diff changeset
364 for (i in levels(factor(levels_table$level))) {
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artbio
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diff changeset
365 fit_res$contribution[, levels_table$element_identifier[levels_table$level == i]] -> worklist[[i]]
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artbio
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diff changeset
366 sum <- rowSums(as.data.frame(worklist[[i]]))
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artbio
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diff changeset
367 worklist[[i]] <- cbind(worklist[[i]], sum)
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artbio
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diff changeset
368 worklist[[i]] <- worklist[[i]][order(worklist[[i]][, "sum"], decreasing = T), ]
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
artbio
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diff changeset
369 worklist[[i]] <- worklist[[i]][1:opt$signum, ]
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artbio
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diff changeset
370 worklist[[i]] <- worklist[[i]][, -length(as.data.frame(worklist[[i]]))]
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artbio
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371 }
e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710"
artbio
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diff changeset
372 worklist <- as.data.frame(melt(worklist))
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artbio
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373 worklist[, 2] <- paste0(worklist[, 4], " - ", worklist[, 2])
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artbio
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374 }
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artbio
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diff changeset
375
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artbio
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376 colnames(worklist) <- c("signature", "sample", "value", "level")
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artbio
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diff changeset
377 worklist <- as.data.frame(worklist %>% group_by(sample) %>% mutate(value = value / sum(value) * 100))
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artbio
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diff changeset
378 worklist$pos <- cumsum(worklist$value) - worklist$value / 2
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artbio
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diff changeset
379 worklist$label <- factor(worklist$signature)
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artbio
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diff changeset
380 worklist$signature <- factor(worklist$signature)
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artbio
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diff changeset
381 p7 <- ggplot(worklist, aes(x = "", y = value, group = signature, fill = signature)) +
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artbio
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diff changeset
382 geom_bar(width = 1, stat = "identity") +
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artbio
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diff changeset
383 geom_text(aes(label = label), position = position_stack(vjust = 0.5), color = "black", size = 3) +
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artbio
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diff changeset
384 coord_polar("y", start = 0) + facet_wrap(.~sample) +
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artbio
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diff changeset
385 labs(x = "", y = "Samples", fill = tag) +
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artbio
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diff changeset
386 scale_fill_manual(name = paste0(opt$signum, " most contributing\nsignatures\n(in each label/tissue)"),
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artbio
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diff changeset
387 values = signature_colors[levels(worklist$signature)],
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artbio
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diff changeset
388 labels = names(signature_colors[levels(worklist$signature)])) +
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artbio
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diff changeset
389 theme(axis.text = element_blank(),
e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710"
artbio
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diff changeset
390 axis.ticks = element_blank(),
e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710"
artbio
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diff changeset
391 panel.grid = element_blank())
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e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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diff changeset
392 grid.arrange(p7)
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artbio
parents: 0
diff changeset
393
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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diff changeset
394 # Plot relative contribution of the cancer signatures in each sample as a heatmap with sample clustering
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artbio
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diff changeset
395 if (length(vcf_paths) > 1) {
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artbio
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diff changeset
396 p8 <- plot_contribution_heatmap(fit_res$contribution, cluster_samples = TRUE, method = "complete")
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
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diff changeset
397 grid.arrange(p8)
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artbio
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diff changeset
398 }
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artbio
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diff changeset
399
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artbio
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diff changeset
400 # export relative contribution matrix
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artbio
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diff changeset
401 if (!is.na(opt$sig_contrib_matrix)) {
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artbio
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diff changeset
402 output_table <- t(fit_res$contribution) / rowSums(t(fit_res$contribution))
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artbio
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diff changeset
403 if (length(levels(factor(levels_table$level))) > 1) {
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artbio
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diff changeset
404 output_table <- data.frame(sample = paste0(metadata_table[metadata_table$element_identifier == colnames(fit_res$contribution),
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
artbio
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diff changeset
405 3], "-", colnames(fit_res$contribution)),
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artbio
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diff changeset
406 output_table)
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artbio
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diff changeset
407 colnames(output_table) <- gsub("X", "SBS", colnames(output_table))
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artbio
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diff changeset
408 } else {
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artbio
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diff changeset
409 output_table <- data.frame(sample = rownames(output_table), output_table)
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
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diff changeset
410 colnames(output_table) <- gsub("X", "SBS", colnames(output_table))
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artbio
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diff changeset
411 }
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artbio
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diff changeset
412 write.table(output_table, file = opt$sig_contrib_matrix, sep = "\t", quote = F, row.names = F)
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artbio
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diff changeset
413 }
7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460"
artbio
parents: 10
diff changeset
414
2
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
415 # calculate all pairwise cosine similarities
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e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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diff changeset
416 cos_sim_ori_rec <- cos_sim_matrix(pseudo_mut_mat, fit_res$reconstructed)
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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
417 # extract cosine similarities per sample between original and reconstructed
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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418 cos_sim_ori_rec <- as.data.frame(diag(cos_sim_ori_rec))
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419
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420 # 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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421 # 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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422 # 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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423 # 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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424 # 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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425 # the COSMIC signatures. You could use, for example, cosine similarity of 0.95 as a cutoff.
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426
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aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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427 # Adjust data frame for plotting with gpplot
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428 colnames(cos_sim_ori_rec) <- "cos_sim"
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
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429 cos_sim_ori_rec$sample <- row.names(cos_sim_ori_rec)
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aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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430 # Make barplot
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431 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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432 geom_bar(stat = "identity", fill = "skyblue4") +
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433 coord_cartesian(ylim = c(0.8, 1)) +
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434 # coord_flip(ylim=c(0.8,1)) +
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435 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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436 xlab("") +
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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437 # 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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438 # xlim(rev(levels(factor(cos_sim_ori_rec$sample)))) +
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439 theme_bw() +
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440 theme(panel.grid.minor.y = element_blank(),
56c8869a231e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
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441 panel.grid.major.y = element_blank()) +
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442 # Add cut.off line
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443 geom_hline(aes(yintercept = .95))
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444 grid.arrange(p9, top = textGrob("Similarity between true profiles and profiles reconstructed with elementary signatures", gp = gpar(fontsize = 12, font = 3)))
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445 dev.off()
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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446 }
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e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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447
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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448
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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449 # 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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450 if (!is.null(opt$rdata)) {
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451 save.image(file = opt$rdata)
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452 }