update to BC devel

PoisonAlien · Sep 27, 2024 · 6c5293a · 6c5293a
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diff --git 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
@@ -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
@@ -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
@@ -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,