Mercurial > repos > artbio > cpm_tpm_rpk
annotate cpm_tpm_rpk.R @ 1:b74bab5157c4 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
author | artbio |
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date | Tue, 05 Feb 2019 19:51:38 -0500 |
parents | 35d032c46a4e |
children | 563337e780ce |
rev | line source |
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0
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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1 if (length(commandArgs(TRUE)) == 0) { |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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2 system("Rscript cpm_tpm_rpk.R -h", intern = F) |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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3 q("no") |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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4 } |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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5 |
1
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
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6 |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
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7 # load packages that are provided in the conda env |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
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8 options( show.error.messages=F, |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
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9 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
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10 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
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11 warnings() |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
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12 library(optparse) |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
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13 library(ggplot2) |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
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14 library(reshape2) |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
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15 library(Rtsne) |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
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16 |
0
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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17 |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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18 |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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19 #Arguments |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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20 option_list = list( |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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21 make_option( |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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22 c("-d", "--data"), |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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23 default = NA, |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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24 type = 'character', |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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25 help = "Input file that contains count values to transform" |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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26 ), |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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27 make_option( |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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28 c("-t", "--type"), |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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29 default = 'cpm', |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
30 type = 'character', |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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31 help = "Transformation type, either cpm, tpm or rpk [default : '%default' ]" |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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32 ), |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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33 make_option( |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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34 c("-s", "--sep"), |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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35 default = '\t', |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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36 type = 'character', |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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37 help = "File separator [default : '%default' ]" |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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38 ), |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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39 make_option( |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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40 c("-c", "--colnames"), |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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41 default = TRUE, |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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42 type = 'logical', |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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43 help = "Consider first line as header ? [default : '%default' ]" |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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44 ), |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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45 make_option( |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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46 c("-f", "--gene"), |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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47 default = NA, |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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48 type = 'character', |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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49 help = "Two column of gene length file" |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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50 ), |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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51 make_option( |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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52 c("-a", "--gene_sep"), |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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53 default = '\t', |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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54 type = 'character', |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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55 help = "Gene length file separator [default : '%default' ]" |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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56 ), |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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57 make_option( |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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58 c("-b", "--gene_header"), |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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59 default = TRUE, |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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60 type = 'logical', |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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61 help = "Consider first line of gene length as header ? [default : '%default' ]" |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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62 ), |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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63 make_option( |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
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64 c("-l", "--log"), |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
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65 default = FALSE, |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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66 type = 'logical', |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
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67 help = "Should be log transformed as well ? (log2(data +1)) [default : '%default' ]" |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
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68 ), |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
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69 make_option( |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
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70 c("-o", "--out"), |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
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71 default = "res.tab", |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
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72 type = 'character', |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
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73 help = "Output name [default : '%default' ]" |
1
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
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74 ), |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
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75 make_option( |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
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76 "--tsne", |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
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77 default = FALSE, |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
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78 type = 'logical', |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
79 help = "performs T-SNE [default : '%default' ]" |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
80 ), |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
81 make_option( |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
82 "--seed", |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
83 default = 42, |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
84 type = 'integer', |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
85 help = "Seed value for reproducibility [default : '%default' ]" |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
86 ), |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
87 make_option( |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
88 "--perp", |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
89 default = 5.0, |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
90 type = 'numeric', |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
91 help = "perplexity [default : '%default' ]" |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
92 ), |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
93 make_option( |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
94 "--theta", |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
95 default = 1.0, |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
96 type = 'numeric', |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
97 help = "theta [default : '%default' ]" |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
98 ), |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
99 make_option( |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
100 c("-D", "--tsne_out"), |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
101 default = "tsne.pdf", |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
102 type = 'character', |
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
103 help = "T-SNE pdf [default : '%default' ]" |
0
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
104 ) |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
105 ) |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
106 |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
107 opt = parse_args(OptionParser(option_list = option_list), |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
108 args = commandArgs(trailingOnly = TRUE)) |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
109 |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
110 if (opt$data == "" & !(opt$help)) { |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
111 stop("At least one argument must be supplied (count data).\n", |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
112 call. = FALSE) |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
113 } else if ((opt$type == "tpm" | opt$type == "rpk") & opt$gene == "") { |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
114 stop("At least two arguments must be supplied (count data and gene length file).\n", |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
115 call. = FALSE) |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
116 } else if (opt$type != "tpm" & opt$type != "rpk" & opt$type != "cpm") { |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
117 stop("Wrong transformation requested (--type option) must be : cpm, tpm or rpk.\n", |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
118 call. = FALSE) |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
119 } |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
120 |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
121 if (opt$sep == "tab") {opt$sep = "\t"} |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
122 if (opt$gene_sep == "tab") {opt$gene_sep = "\t"} |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
123 |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
124 cpm <- function(count) { |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
125 t(t(count) / colSums(count)) * 1000000 |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
126 } |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
127 |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
128 |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
129 rpk <- function(count, length) { |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
130 count / (length / 1000) |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
131 } |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
132 |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
133 tpm <- function(count, length) { |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
134 RPK = rpk(count, length) |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
135 perMillion_factor = colSums(RPK) / 1000000 |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
136 TPM = RPK / perMillion_factor |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
137 return(TPM) |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
138 } |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
139 |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
140 data = read.table( |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
141 opt$data, |
1
b74bab5157c4
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents:
0
diff
changeset
|
142 header = opt$colnames, |
0
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
143 row.names = 1, |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
144 sep = opt$sep |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
145 ) |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
146 |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
147 if (opt$type == "tpm" | opt$type == "rpk") { |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
148 gene_length = as.data.frame( |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
149 read.table( |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
150 opt$gene, |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
151 h = opt$gene_header, |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
152 row.names = 1, |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
153 sep = opt$gene_sep |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
154 ) |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
155 ) |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
156 gene_length = as.data.frame(gene_length[match(rownames(data), rownames(gene_length)), ], rownames(data)) |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff
changeset
|
157 } |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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158 |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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159 |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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160 if (opt$type == "cpm") |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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161 res = cpm(data) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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162 if (opt$type == "tpm") |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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163 res = as.data.frame(apply(data, 2, tpm, length = gene_length), row.names = rownames(data)) |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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164 if (opt$type == "rpk") |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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165 res = as.data.frame(apply(data, 2, rpk, length = gene_length), row.names = rownames(data)) |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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166 colnames(res) = colnames(data) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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167 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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168 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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169 if (opt$log == TRUE) { |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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170 res = log2(res + 1) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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171 } |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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172 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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173 write.table( |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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174 cbind(Features = rownames(res), res), |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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175 opt$out, |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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176 col.names = opt$colnames, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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177 row.names = F, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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178 quote = F, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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179 sep = "\t" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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180 ) |
35d032c46a4e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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181 |
1
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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182 ## |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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183 if (opt$tsne == TRUE) { |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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184 df = cpm(data) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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185 # filter and transpose df for tsne |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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186 df = df[rowSums(df) != 0,] # remove lines without information (with only 0 counts) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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187 tdf = t(df) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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188 tdf = log2(tdf + 1) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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189 # make tsne and plot results |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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190 set.seed(opt$seed) ## Sets seed for reproducibility |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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191 # Run TSNE |
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192 tsne_out <- Rtsne(tdf, perplexity=opt$perp, theta=opt$theta) # |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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193 embedding <- as.data.frame(tsne_out$Y) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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194 embedding$Class <- as.factor(sub("Class_", "", rownames(tdf))) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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195 gg_legend = theme(legend.position="none") |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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196 ggplot(embedding, aes(x=V1, y=V2)) + |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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197 geom_point(size=1.25, color='red') + |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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198 geom_text(aes(label=Class),hjust=-0.2, vjust=-0.5, size=2.5, color='darkblue') + |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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199 gg_legend + |
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200 xlab("") + |
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201 ylab("") + |
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202 ggtitle('t-SNE of data (log2CPM transformed)') |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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203 ggsave(file=opt$tsne_out, device="pdf") |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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204 } |
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205 |
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206 |
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207 |
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208 |
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209 |
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210 |
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211 |
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212 |
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213 |
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214 |
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215 |
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216 |