Mercurial > repos > artbio > mutational_patterns
changeset 16:31e7a33ecd71 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 9deb533aabc9dc24bb88b98c57e242785142df75"
| author | artbio |
|---|---|
| date | Mon, 04 Oct 2021 00:35:06 +0000 |
| parents | 8182d1625433 |
| children | 8c6ee1c2248f |
| files | mutational_patterns.R mutational_patterns.xml test-data/cosmic_output1.pdf test-data/cosmic_output2.pdf test-data/cosmic_output_v3.pdf test-data/denovo_1.RData test-data/denovo_output1.pdf test-data/sig_contrib_table.tsv test-data/sig_contrib_table_v3.tsv test-data/spectrum_output1.pdf |
| diffstat | 10 files changed, 18 insertions(+), 18 deletions(-) [+] |
line wrap: on
line diff
--- a/mutational_patterns.R Sun Oct 03 09:29:04 2021 +0000 +++ b/mutational_patterns.R Mon Oct 04 00:35:06 2021 +0000 @@ -220,23 +220,23 @@ pdf(opt$output_cosmic, paper = "special", width = 11.69, height = 11.69) pseudo_mut_mat <- mut_mat + 0.0001 # First add a small psuedocount to the mutation count matrix if (opt$cosmic_version == "v2") { - sp_url <- paste("https://cancer.sanger.ac.uk/cancergenome/assets/", "signatures_probabilities.txt", sep = "") + sp_url <- "https://cancer.sanger.ac.uk/signatures/documents/420/COSMIC_v2_SBS_GRCh38.txt" cancer_signatures <- read.table(sp_url, sep = "\t", header = TRUE) - new_order <- match(row.names(pseudo_mut_mat), cancer_signatures$Somatic.Mutation.Type) + new_order <- match(row.names(pseudo_mut_mat), cancer_signatures$Type) cancer_signatures <- cancer_signatures[as.vector(new_order), ] - row.names(cancer_signatures) <- cancer_signatures$Somatic.Mutation.Type - cancer_signatures <- as.matrix(cancer_signatures[, 4:33]) - colnames(cancer_signatures) <- gsub("Signature.", "", colnames(cancer_signatures)) # shorten signature labels + row.names(cancer_signatures) <- cancer_signatures$Type + cancer_signatures <- as.matrix(cancer_signatures[, 2:31]) + colnames(cancer_signatures) <- gsub("Signature_", "", colnames(cancer_signatures)) # shorten signature labels cosmic_tag <- "Signatures (Cosmic v2, March 2015)" cosmic_colors <- col_vector[1:30] names(cosmic_colors) <- colnames(cancer_signatures) } else { - sp_url <- "https://raw.githubusercontent.com/ARTbio/startbio/master/sigProfiler_SBS_signatures_2019_05_22.tsv" + sp_url <- "https://cancer.sanger.ac.uk/signatures/documents/431/COSMIC_v3_SBS_GRCh38.txt" cancer_signatures <- read.table(sp_url, sep = "\t", header = TRUE) - new_order <- match(row.names(pseudo_mut_mat), cancer_signatures$Somatic.Mutation.Type) + new_order <- match(row.names(pseudo_mut_mat), cancer_signatures$Type) cancer_signatures <- cancer_signatures[as.vector(new_order), ] - row.names(cancer_signatures) <- cancer_signatures$Somatic.Mutation.Type - cancer_signatures <- as.matrix(cancer_signatures[, 4:70]) + row.names(cancer_signatures) <- cancer_signatures$Type + cancer_signatures <- as.matrix(cancer_signatures[, 2:68]) colnames(cancer_signatures) <- gsub("SBS", "", colnames(cancer_signatures)) # shorten signature labels cosmic_tag <- "Signatures (Cosmic v3, May 2019)" cosmic_colors <- col_vector[1:67]
--- a/mutational_patterns.xml Sun Oct 03 09:29:04 2021 +0000 +++ b/mutational_patterns.xml Mon Oct 04 00:35:06 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy0"> +<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy1"> <description>from genomic variations in vcf files</description> <requirements> <requirement type="package" version="3.2.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement>
--- a/test-data/sig_contrib_table.tsv Sun Oct 03 09:29:04 2021 +0000 +++ b/test-data/sig_contrib_table.tsv Mon Oct 04 00:35:06 2021 +0000 @@ -1,5 +1,5 @@ sample s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30 -ovary-I.vcf 0.11366483685008 0.0109938593266657 0.261053482791866 0 0.102195880307416 0.00220769920517984 0 0.121596331607151 0.0667024002680757 0 0.0463559883343337 0.0477514837858505 0.00153570456409855 0 0.0196723565031216 0.125168078635871 0 0 0 0 0 0 0 0 0.056462960047836 0 0.000124367513387182 0.0245145702590675 0 0 -ovary-H.vcf 0.108363933620392 0.0163896275457592 0.219669872246722 0 0.267579919199733 0 0 0.0644683944374041 0.0647530723986353 0 0.0255690291284295 0 0.0096156971999939 0 0 0.16879742588098 0 0 0 0 0 0 0 0 0.0144022954450145 0 0.00628915179499457 0.0341015811019413 0 0 -lung-G.vcf 0.216042386729494 0.0163285606624902 0.174782553623772 0 0.243519493008331 0 0 0.00859703357366864 0.122147877946073 0 0.031028717517658 0.0398485713623127 0 0 0 0.0426507272713916 0 0 0.0331593375475991 0 0 0 0 0 0.0690376730723399 0 0.00121112083973226 0.00164594684513809 0 0 -lung-F.vcf 0.277447721812717 0.00581547878718051 0.177348626019748 0 0.1009356992577 0 0 0.0920458551898083 0.0183096024827367 0 0.0300240298284301 0.00396441475927008 0 0 0 0.195845126035802 0 0 0 0 0 0 0 0 0.0270963890910293 0 0.0049085436021671 0.041321577314175 0 0.0249369358192356 +ovary-I.vcf 0.107676737465178 0.0107477401085281 0.263118370815298 0 0.0975192598491968 0.00654300960428024 0 0.121325654310372 0.0675812234604709 0 0.0475946682228466 0.0483240788134274 0.00116766365611527 0 0.0195773794486755 0.128367970358363 0 0 0 0 0 0 0 0 0.0564468988265929 0 0.000297382010539655 0.0237119630501146 0 0 +ovary-H.vcf 0.105483533021363 0.0160722050763363 0.220294683323486 0 0.270646531625838 0 0 0.0632630764001629 0.0651960109780565 0 0.0265849338024135 0 0.00937728828228106 0 0 0.169077458531394 0 0 0 0 0 0 0 0 0.0141372418969508 0 0.0064233897483352 0.0334436473133834 0 0 +lung-G.vcf 0.210828794798222 0.0160042182355152 0.174216713183146 0 0.248848735805233 0 0 0.0079146795135654 0.122852241624819 0 0.0316731744534412 0.0400882001887818 0 0 0 0.0415901687752403 0 0 0.0349534584507835 0 0 0 0 0 0.0686079325155911 0 0.0013880107407027 0.00103367171495887 0 0 +lung-F.vcf 0.272200051777229 0.00523782090972898 0.176429226414213 0 0.107322684968036 0 0 0.0922420552015618 0.0176321903825532 0 0.0308049189266778 0.00421945577891649 0 0 0 0.195343895329217 0 0 0 0 0 0 0 0 0.026099693090191 0 0.0050497865751646 0.0410158172026456 0 0.0264024034438657
--- a/test-data/sig_contrib_table_v3.tsv Sun Oct 03 09:29:04 2021 +0000 +++ b/test-data/sig_contrib_table_v3.tsv Mon Oct 04 00:35:06 2021 +0000 @@ -1,5 +1,5 @@ sample s1 s2 s3 s4 s5 s6 s7a s7b s7c s7d s8 s9 s10a s10b s11 s12 s13 s14 s15 s16 s17a s17b s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30 s31 s32 s33 s34 s35 s36 s37 s38 s39 s40 s41 s42 s43 s44 s45 s46 s47 s48 s49 s50 s51 s52 s53 s54 s55 s56 s57 s58 s59 s60 s84 s85 -ovary-I.vcf 0.0292102144556227 0 0 0.00144007322742414 0 0.0504390788292217 0.00194348408726673 0 0.0525707708741538 0 0.0914724303738797 0 0.000832163233383592 0 0 0 0.00842487825711237 0 0.0135094432679645 0.0366586044772389 0 0 0.0185740536261001 0.00229375063200434 0 0.00970266938170121 0 0 0.00599759333539559 0.0421114673613094 0.0114310779471638 0 0.0135490307866796 0 0.0296793772659665 0.0277524342410843 0.0454269664537971 0.00938724128600892 0.0136144947369238 0 0 0.0833465920869942 0 0.137690178135469 0 0 0 0.00953146514960113 0.0202102619863343 0 0 0 0 4.88486910392704e-05 0.00760389505513268 0.0232276886439185 0 0 0.013878903464201 0 0 0.058642750046278 0.129529443690174 0.000268674913454976 0 0 0 -ovary-H.vcf 0.0523809674402057 0 0 0.0073487755957751 0 0 0.00289534105048845 0 0.028141106223541 0.00357241172591758 0.0900610723552876 0 0.00471257812773401 0 0 0 0.0152354080005807 0 0 0.056026125482423 0 0.00257191790029753 0 0.0165305233542475 0 0.000141899985605957 0 0 0.00488001259024111 0.00918859610852697 0.00475106755263085 0.00663010539344573 0.017109685037444 0 0.04731550745362 0.00365691117000763 0.0328768691449399 0.0120314432988265 0.0167811048132417 0 0 0.0950039544413254 0 0.137196255594851 0 0 0 0 0.0597953621090927 0 0 0 0 4.23604750551013e-05 0.0121309998776711 0.00973226374395621 0 0.00222509583262053 0.0251951439030708 0.0118558225702647 0 0.0846395405044328 0.125310604958315 0.00203316618431609 0 0 0 -lung-G.vcf 0.0873029632099988 0 0 0 0 0.0479104551341112 0.00776867305403075 0 0.0313814579173264 0 0.0609850595672004 0.0172622613117254 0 0.00012666179996385 0 0 0.00765587561722924 0 0 0.0278690467140333 0.000454577309760022 0 0.0206812596225624 0.0359443715017539 0 0.0120875070366763 0.00187879472330278 0 0.00683351257522683 0.0494238708587332 0 0 0 0 0.0480909479022159 0.00328524460204372 0.037243337279276 0.000684746817696913 0.0170460736503824 0 0 0.120242044269861 0 0.0912990485885233 0 0 0.00198825222515588 0 0.00367924369018231 0 0 0.00127107492891469 0 0 0 0.0337265499103692 0 0.00040976068762453 0.035143574313439 0 0 0.080043690949342 0.096390826001613 0 0.00205878889713283 0.0118304473325925 0 -lung-F.vcf 0.130972951527932 0 0.0761687896979774 0 0 0 0 0 0.0340317364900266 0 0.0786848101409268 0 0.00232431375487017 0.00924283426133058 0 0 0 0 0 0.0454990529437777 0 0 0.0111440674145277 0.0156984823484767 0 0.00368064004289289 0.00101383322501298 0 0.00769126266914517 0.0114608643279846 0 0.000168984385199036 0.0236023336834282 0 0.064421387701359 0.00659674935231646 0.036711297327122 0.00568327050616103 0.00956407247236277 0 0 0.0874117950073058 0 0.0752825647107504 0 0 0 0.00313252048097358 0.0213677245928594 0 0 0.0221471177980541 0 0.000825664351643732 0 0.0132117228813227 0 0.00204298080257053 0.0390511638798427 0 0 0.0245617897055234 0.122391156939586 0.00304240662816143 0 0.0111696579485762 0 +ovary-I.vcf 0.0261662312700287 0 0 0.00540922040548445 0 0.0554522494221051 0.0015054005135302 0 0.0527698220499384 0 0.0887078997707257 0 0.000907076161215129 0 0 0 0.00816538925821039 0 0.0128589414347678 0.0380260440755711 0 0 0.0173905924247456 0.001707488229021 0 0.010276473882261 0 0 0.00537132652951311 0.0418328062226971 0.011268103748697 0 0.013513567633232 0 0.0299817999935266 0.0290828169035887 0.0455904351684802 0.00911446107696196 0.0142491074457184 0 0 0.0828680955875177 0 0.137846212289707 0 0 0 0.00955362702540194 0.0176518216878586 0 0 0 0 0 0.00791168443668074 0.023401746173643 0 0 0.0142889494092746 0 0 0.0589804306629367 0.127565493753874 0.00058468535308627 0 0 0 +ovary-H.vcf 0.0514943738497272 0 0 0.0087020810819626 0 0 0.00236410365956529 0 0.0283100865280861 0.00330015778410193 0.0876336183320928 0 0.00461986640013499 0 0 0 0.0149334722781705 0 0 0.0575304849089614 0 0.00251629772375885 0 0.0165652645823303 0 0.000624306444994269 0 0 0.00504372393616242 0.00966085594196363 0.00415555408979927 0.00663515443687386 0.0171493644187634 0 0.0481611871648976 0.00444934777109341 0.0328633359412982 0.0116426528342991 0.0171447988100082 0 0 0.0946683632396481 0 0.137633236641122 0 0 0 0 0.0602320275961475 0 0 0 0 0 0.0124382204627417 0.0101014447648236 0 0.00234093513264533 0.0255780469333522 0.0118621125591813 0 0.0844080841563258 0.123178981782342 0.00205845781262428 0 0 0 +lung-G.vcf 0.0835415571466835 0 0 0 0 0.0531396303027374 0.00733219232339216 0 0.0313762292215084 0 0.0606428164890939 0.0176603522234399 0 0.000123110879620826 0 0 0.00735095968187644 0 0 0.0290566556597906 0.00029875750108526 0 0.0203972540873668 0.0355580201715423 0 0.0123438369843411 0.00148831528108934 0 0.00702152929618746 0.0500581225968108 0 0 0 0 0.0483376674495861 0.00503826980581789 0.0375230365596794 0.000365640786534471 0.0173540188566111 0 0 0.119562508095986 0 0.0922495052872749 0 0 0.00186662484782185 0 0.00198383177758492 0 0 0.0016907139525808 0 0 0 0.0339551728551291 0 0.000506019602171982 0.0354612532013092 0 0 0.0800934470527665 0.0943176689178333 0 0.00204207638725024 0.0102632047174961 0 +lung-F.vcf 0.129733671535086 0 0.0756510632174742 0 0 0 0 0 0.0340346028561247 0 0.0771217892059738 0 0.00227780162121716 0.00924261610588687 0 0 0 0 0 0.0465201871969074 0 0 0.0110305938436319 0.0158255469126101 0 0.00374844346904832 0.00146787555295699 0 0.00847802739839135 0.0105235337001421 0 0.000114895596046716 0.0236577247003424 0 0.0645253165188412 0.00780877511904059 0.0367599879858517 0.00522232526398284 0.0100399736075406 0 0 0.087309725420689 0 0.0759894281641185 0 0 0.000534487830683315 0.00298777004029269 0.0229584360721825 0 0 0.0217298493319228 0 0.00070999042925293 0 0.0141214288614859 0 0.00249376674671315 0.0393307390657661 0 0 0.0241692429399726 0.120513106763722 0.00304686844730181 0 0.0103204084787993 0