From 6c5293ae547daeaf5fb19ec200e0a3a30a734c39 Mon Sep 17 00:00:00 2001 From: Anand Mayakonda Date: Fri, 27 Sep 2024 16:30:50 +0200 Subject: [PATCH] update to BC devel --- DESCRIPTION | 2 +- inst/NEWS.md | 68 +---------------------------------------- inst/old_news | 65 +++++++++++++++++++++++++++++++++++++++ vignettes/oncoplots.Rmd | 18 +++++++---- 4 files changed, 79 insertions(+), 74 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4ba80a1..ee44f24 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: maftools Title: Summarize, Analyze and Visualize MAF Files -Version: 2.20.1 +Version: 2.21.1 Date: 2021-04-30 Authors@R: person(given = "Anand", diff --git a/inst/NEWS.md b/inst/NEWS.md index 09ebf24..69d2ffb 100644 --- a/inst/NEWS.md +++ b/inst/NEWS.md @@ -1,4 +1,4 @@ -# CHANGES IN VERSION 2.20.1 +# CHANGES IN VERSION 2.21.1 (GitHub master branch - version bumped from 2.18.1 to 2.20.1 to match BC release branch) ## BUG FIXES @@ -17,72 +17,6 @@ - Changed default signature database to SBS_v3.4 (from legacy) - Update `tmb` function - ## NEW FUNCTIONS - `gisticCompare()` for comparing two GISTIC objects - `segSummarize()` for summarizing DNAcopy segments - -# CHANGES IN VERSION 2.18.0 -(Bioconductor release branch - 2.20.0) - -## NEW FUNCTIONS -- `pathways` and `plotPathways`for summarizing & visualizing pathways Issue: [956](https://github.com/PoisonAlien/maftools/issues/956) -- `coGisticChromPlot` for plotting two GISTIC objects side-by-side. PR by [biosunsci](https://github.com/biosunsci) [954](https://github.com/PoisonAlien/maftools/pull/954) -- `readGistic` can take gistic output directory as an input. PR by [biosunsci](https://github.com/biosunsci) [954](https://github.com/PoisonAlien/maftools/pull/954) - -## BUG FIXES -- Bug fixes while processing custom pathways -- Bug fix in `oncoplot` for drawing borders. [958](https://github.com/PoisonAlien/maftools/issues/958) -- Bug fix in `plotSignatures` for hardcoded axis limits. [949](https://github.com/PoisonAlien/maftools/issues/949) -- Bug fix in `mafSurvival` legend when samples argument is give. [937](https://github.com/PoisonAlien/maftools/issues/937) -- Bug fix in `subsetMaf` while handling only CNV events. [908](https://github.com/PoisonAlien/maftools/issues/908) -- Error handling when no deep/shallow CNV events found. [899](https://github.com/PoisonAlien/maftools/issues/899) -- Bug fix in `oncoplot` for duplicated values in gene list. [889](https://github.com/PoisonAlien/maftools/issues/889) - -## ENHANCEMENTS -- Added argument `collapsePathway` to `oncoplot`. Issue: [956](https://github.com/PoisonAlien/maftools/issues/956) -- Improved `annovarToMaf` with better handling of indels and `Variant_Type`. Issue: [940](https://github.com/PoisonAlien/maftools/issues/940) -- Include absolute contribution of each signature in `extractSignatures` output. Issue: [939](https://github.com/PoisonAlien/maftools/issues/939) -- Added `tsbToPIDs` for custom names in `oncoplot`. Issue: Issue: [936](https://github.com/PoisonAlien/maftools/issues/936) -- Added `DSEL` protein to the database. Issue: [933](https://github.com/PoisonAlien/maftools/issues/933) -- Added `MUC3A` protein to the database. Issue: [932](https://github.com/PoisonAlien/maftools/issues/932) -- Added `showOnlyPathway` argument to `oncoplot` -- Added `pathdb` argument to `PlotOncogenicPathways`. Issue: [923](https://github.com/PoisonAlien/maftools/issues/923) -- Emit warnings when fishers test can not be performed during `somaticInteractions`. Issue: [921](https://github.com/PoisonAlien/maftools/issues/921) -- Added `leftMar` and `topMar` arguments to `somaticInteractions`. Issue: [913](https://github.com/PoisonAlien/maftools/issues/913) -- Added `toptBarLims` argument to oncoplot. Issue: [910](https://github.com/PoisonAlien/maftools/issues/910) -- Added `data` argument to `lollipopPlot` function. Issue: [894](https://github.com/PoisonAlien/maftools/issues/894) -- Added `sortByM1` and `sortByM2` argument to `coOncoplot`. Issue: [888](https://github.com/PoisonAlien/maftools/issues/888) -- Added arguments `leftBarVline`, `leftBarVlineCol`, `rightBarVline`, `rightBarVlineCol` `topBarHline` `topBarHlineCol` to `oncoplot`. Issue: [874](https://github.com/PoisonAlien/maftools/issues/874) -- Added `revPal` argument to `somaticInteractions`. Issue: [859](https://github.com/PoisonAlien/maftools/issues/859) -- Fix legend and color codes for numeric annotations in `oncoplot`. Issue: [363](https://github.com/PoisonAlien/maftools/issues/363) - -# CHANGES IN VERSION 2.16.0 - -- No changes - -# CHANGES IN VERSION 2.14.0 - -- No changes - -# CHANGES IN VERSION 2.12.05 - -## BUG FIXES -- genes parameter in `plotClusters` can't accept list of genes. Issue: [828](https://github.com/PoisonAlien/maftools/issues/828) -- Ignore NAs while generating `trinucleotideMatrix`. Issue: [841](https://github.com/PoisonAlien/maftools/issues/841) - -## ENHANCEMENTS -- Added protein structure for NRIP1. Issue: [832](https://github.com/PoisonAlien/maftools/issues/832) -- Added protein structure for SETBP1. Issue: [696](https://github.com/PoisonAlien/maftools/issues/696) - -# CHANGES IN VERSION 2.12.00 -(BC 3.15) - -## NEW FUNCTIONS -- `gtMarkers`, `prepAscat`, `prepAscat_t`, `segmentLogR` provides interface to copy number analysis with ASCAT. -- `plotMosdepth` and `plotMosdepth_t` processes output generated by Mosdepth and performs copy number analysis with DNAcopy -- `cancerhotspotsAggr` Aggregates `cancerhotspots` reports - -## ENHANCEMENTS -- Added support for plotting adjusted p-values in `somaticInteractions`. Issue: [813](https://github.com/PoisonAlien/maftools/issues/813) -- Added support for the protein structure `BECN2` Issue: [696](https://github.com/PoisonAlien/maftools/issues/696) diff --git a/inst/old_news b/inst/old_news index 817e19a..23f67cc 100644 --- a/inst/old_news +++ b/inst/old_news @@ -1,3 +1,68 @@ +# CHANGES IN VERSION 2.18.0 +(Bioconductor release branch - 2.20.0) + +## NEW FUNCTIONS +- `pathways` and `plotPathways`for summarizing & visualizing pathways Issue: [956](https://github.com/PoisonAlien/maftools/issues/956) +- `coGisticChromPlot` for plotting two GISTIC objects side-by-side. PR by [biosunsci](https://github.com/biosunsci) [954](https://github.com/PoisonAlien/maftools/pull/954) +- `readGistic` can take gistic output directory as an input. PR by [biosunsci](https://github.com/biosunsci) [954](https://github.com/PoisonAlien/maftools/pull/954) + +## BUG FIXES +- Bug fixes while processing custom pathways +- Bug fix in `oncoplot` for drawing borders. [958](https://github.com/PoisonAlien/maftools/issues/958) +- Bug fix in `plotSignatures` for hardcoded axis limits. [949](https://github.com/PoisonAlien/maftools/issues/949) +- Bug fix in `mafSurvival` legend when samples argument is give. [937](https://github.com/PoisonAlien/maftools/issues/937) +- Bug fix in `subsetMaf` while handling only CNV events. [908](https://github.com/PoisonAlien/maftools/issues/908) +- Error handling when no deep/shallow CNV events found. [899](https://github.com/PoisonAlien/maftools/issues/899) +- Bug fix in `oncoplot` for duplicated values in gene list. [889](https://github.com/PoisonAlien/maftools/issues/889) + +## ENHANCEMENTS +- Added argument `collapsePathway` to `oncoplot`. Issue: [956](https://github.com/PoisonAlien/maftools/issues/956) +- Improved `annovarToMaf` with better handling of indels and `Variant_Type`. Issue: [940](https://github.com/PoisonAlien/maftools/issues/940) +- Include absolute contribution of each signature in `extractSignatures` output. Issue: [939](https://github.com/PoisonAlien/maftools/issues/939) +- Added `tsbToPIDs` for custom names in `oncoplot`. Issue: Issue: [936](https://github.com/PoisonAlien/maftools/issues/936) +- Added `DSEL` protein to the database. Issue: [933](https://github.com/PoisonAlien/maftools/issues/933) +- Added `MUC3A` protein to the database. Issue: [932](https://github.com/PoisonAlien/maftools/issues/932) +- Added `showOnlyPathway` argument to `oncoplot` +- Added `pathdb` argument to `PlotOncogenicPathways`. Issue: [923](https://github.com/PoisonAlien/maftools/issues/923) +- Emit warnings when fishers test can not be performed during `somaticInteractions`. Issue: [921](https://github.com/PoisonAlien/maftools/issues/921) +- Added `leftMar` and `topMar` arguments to `somaticInteractions`. Issue: [913](https://github.com/PoisonAlien/maftools/issues/913) +- Added `toptBarLims` argument to oncoplot. Issue: [910](https://github.com/PoisonAlien/maftools/issues/910) +- Added `data` argument to `lollipopPlot` function. Issue: [894](https://github.com/PoisonAlien/maftools/issues/894) +- Added `sortByM1` and `sortByM2` argument to `coOncoplot`. Issue: [888](https://github.com/PoisonAlien/maftools/issues/888) +- Added arguments `leftBarVline`, `leftBarVlineCol`, `rightBarVline`, `rightBarVlineCol` `topBarHline` `topBarHlineCol` to `oncoplot`. Issue: [874](https://github.com/PoisonAlien/maftools/issues/874) +- Added `revPal` argument to `somaticInteractions`. Issue: [859](https://github.com/PoisonAlien/maftools/issues/859) +- Fix legend and color codes for numeric annotations in `oncoplot`. Issue: [363](https://github.com/PoisonAlien/maftools/issues/363) + +# CHANGES IN VERSION 2.16.0 + +- No changes + +# CHANGES IN VERSION 2.14.0 + +- No changes + +# CHANGES IN VERSION 2.12.05 + +## BUG FIXES +- genes parameter in `plotClusters` can't accept list of genes. Issue: [828](https://github.com/PoisonAlien/maftools/issues/828) +- Ignore NAs while generating `trinucleotideMatrix`. Issue: [841](https://github.com/PoisonAlien/maftools/issues/841) + +## ENHANCEMENTS +- Added protein structure for NRIP1. Issue: [832](https://github.com/PoisonAlien/maftools/issues/832) +- Added protein structure for SETBP1. Issue: [696](https://github.com/PoisonAlien/maftools/issues/696) + +# CHANGES IN VERSION 2.12.00 +(BC 3.15) + +## NEW FUNCTIONS +- `gtMarkers`, `prepAscat`, `prepAscat_t`, `segmentLogR` provides interface to copy number analysis with ASCAT. +- `plotMosdepth` and `plotMosdepth_t` processes output generated by Mosdepth and performs copy number analysis with DNAcopy +- `cancerhotspotsAggr` Aggregates `cancerhotspots` reports + +## ENHANCEMENTS +- Added support for plotting adjusted p-values in `somaticInteractions`. Issue: [813](https://github.com/PoisonAlien/maftools/issues/813) +- Added support for the protein structure `BECN2` Issue: [696](https://github.com/PoisonAlien/maftools/issues/696) + # CHANGES IN VERSION 2.10.05 - Added PALB2 protein structure. Issue: [677](https://github.com/PoisonAlien/maftools/issues/677) diff --git a/vignettes/oncoplots.Rmd b/vignettes/oncoplots.Rmd index f7a640f..100f72a 100644 --- a/vignettes/oncoplots.Rmd +++ b/vignettes/oncoplots.Rmd @@ -191,19 +191,25 @@ oncoplot(maf = laml, genes = aml_genes, clinicalFeatures = 'FAB_classification') More than one annotations can be included by passing them to the argument `clinicalFeatures`. Above plot can be further enhanced by sorting according to annotations. Custom colors can be specified as a list of named vectors for each levels. -```{r oncoplotFABcolors} +```{r oncoplotFABcolors, fig.height=7} #Color coding for FAB classification fabcolors = RColorBrewer::brewer.pal(n = 8,name = 'Spectral') names(fabcolors) = c("M0", "M1", "M2", "M3", "M4", "M5", "M6", "M7") -fabcolors = list(FAB_classification = fabcolors) -print(fabcolors) +#For continuous numrical annotations, use one of the below palettes +# c("Blues", "BuGn", "BuPu", "GnBu", "Greens", "Greys", "Oranges", +# "OrRd", "PuBu", "PuBuGn", "PuRd", "Purples", "RdPu", "Reds", +# "YlGn", "YlGnBu", "YlOrBr", "YlOrRd") + +anno_cols = list(FAB_classification = fabcolors, days_to_last_followup = "Blues") + +print(anno_cols) oncoplot( maf = laml, genes = aml_genes, - clinicalFeatures = 'FAB_classification', + clinicalFeatures = c('FAB_classification', 'days_to_last_followup'), sortByAnnotation = TRUE, - annotationColor = fabcolors + annotationColor = anno_cols ) ``` @@ -296,7 +302,7 @@ oncoplot( maf = laml.plus.gistic, draw_titv = TRUE, pathways = pathways, - clinicalFeatures = c('FAB_classification', 'Overall_Survival_Status'), + clinicalFeatures = c('FAB_classification', 'days_to_last_followup'), sortByAnnotation = TRUE, additionalFeature = c("Tumor_Seq_Allele2", "C"), leftBarData = aml_genes_vaf,