Address #1069 and #1065

PoisonAlien · Nov 4, 2024 · 7c08a05 · 7c08a05
1 parent 79e5cd5
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Showing 5 changed files with 40 additions and 33 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: maftools
 Title: Summarize, Analyze and Visualize MAF Files
-Version: 2.21.2
+Version: 2.22.10
 Date: 2021-04-30
 Authors@R: 
     person(given = "Anand",

diff --git a/R/oncoplot.R b/R/oncoplot.R
@@ -591,6 +591,7 @@ oncoplot = oncoplot = function(maf, top = 20, minMut = NULL, genes = NULL, alter
   if(drawRowBar){
     if(is.null(rightBarData)){
       side_bar_lims = c(0, max(unlist(apply(numMat, 1, function(x) cumsum(table(x[x!=0])))), na.rm = TRUE))
+      rightBarTitle = "No. of samples"
     }else{
       rightBarTitle = colnames(rightBarData)[2]
       colnames(rightBarData) = c('genes', 'exprn')
@@ -621,7 +622,6 @@ oncoplot = oncoplot = function(maf, top = 20, minMut = NULL, genes = NULL, alter
 
       plot(x = NA, y = NA, type = "n", axes = FALSE,
            xlim = side_bar_lims, ylim = c(0, 1), xaxs = "i")
-      rightBarTitle = "No. of samples"
     }
   }
 
@@ -761,8 +761,8 @@ oncoplot = oncoplot = function(maf, top = 20, minMut = NULL, genes = NULL, alter
   }
 
   #Add grids
-  abline(h = (0:ncol(nm)) + 0.5, col = borderCol, lwd = sepwd_genes)
-  abline(v = (0:nrow(nm)) + 0.5, col = borderCol, lwd = sepwd_samples)
+  abline(h = (0:ncol(nm)) + 0.5, col = borderCol, lwd = sepwd_genes, xpd = FALSE)
+  abline(v = (0:nrow(nm)) + 0.5, col = borderCol, lwd = sepwd_samples, xpd = FALSE)
 
   #Add boxes if pathways are opted
   if(!is.null(pathways)){
@@ -1067,7 +1067,7 @@ oncoplot = oncoplot = function(maf, top = 20, minMut = NULL, genes = NULL, alter
 
       #Add grids
       rect(xleft = 0.5, ybottom = (0:(ncol(annotation))) + 0.5, xright = nrow(annotation)+0.5, ytop = (0:(ncol(annotation))) + 0.5, border = annoBorderCol, lwd = 0.7)
-      abline(v = (0:(nrow(nm))) + 0.5, col = annoBorderCol, lwd = sepwd_samples)
+      abline(v = (0:(nrow(nm))) + 0.5, col = annoBorderCol, lwd = sepwd_samples, xpd = FALSE)
       mtext(text = colnames(annotation), side = 4,
             font = 1, line = 0.4, cex = fontSize, las = 2, at = 1:ncol(annotation))
 

diff --git a/R/print_mat.R b/R/print_mat.R
@@ -243,8 +243,8 @@ print_mat = function(maf, genes, removeNonMutated = TRUE, colors = NULL,
   }
 
   #Add grids
-  abline(h = (1:ncol(nm)) + 0.5, col = borderCol, lwd = sepwd_genes)
-  abline(v = (1:nrow(nm)) + 0.5, col = borderCol, lwd = sepwd_samples)
+  abline(h = (1:ncol(nm)) + 0.5, col = borderCol, lwd = sepwd_genes, xpd = FALSE)
+  abline(v = (1:nrow(nm)) + 0.5, col = borderCol, lwd = sepwd_samples, xpd = FALSE)
   title(title, cex.main = title_size, outer = FALSE, font = 2)
 
   # mtext(text = colnames(nm), side = 2, at = 1:ncol(nm),
@@ -330,8 +330,8 @@ print_mat = function(maf, genes, removeNonMutated = TRUE, colors = NULL,
     }
 
     #Add grids
-    abline(h = (1:ncol(nm)) + 0.5, col = "white", lwd = sepwd_genes)
-    abline(v = (1:nrow(nm)) + 0.5, col = "white", lwd = sepwd_samples)
+    abline(h = (1:ncol(nm)) + 0.5, col = "white", lwd = sepwd_genes, xpd = FALSE)
+    abline(v = (1:nrow(nm)) + 0.5, col = "white", lwd = sepwd_samples, xpd = FALSE)
     if(plot2){
       mtext(text = colnames(annotation), side = 4,
             font = 1, line = 0.4, cex = fontSize, las = 2, at = 1:ncol(annotation))

diff --git a/inst/NEWS.md b/inst/NEWS.md
@@ -1,26 +1,5 @@
-# CHANGES IN VERSION 2.21.2
+# CHANGES IN VERSION 2.22.10
 
 ## BUG FIXES
-- Bug fix in using `keepGeneOrder` in `coOncoplot()`. Issue: [1061](https://github.com/PoisonAlien/maftools/issues/1061)
-- Bug fix in using `selectedPathways` in `oncoplot()`. Issue: [1041](https://github.com/PoisonAlien/maftools/issues/1041)
-- Add an error message when bai files are missing `sampleSwaps()`. Issue: [1028](https://github.com/PoisonAlien/maftools/issues/1028)
-- Bug fix in `tmb` while handling multiple MAFs. Issue: [1018](https://github.com/PoisonAlien/maftools/issues/1018)
-- Handle missing `NA`s while sub-setting for ranges. Issue: [1013](https://github.com/PoisonAlien/maftools/issues/1013)
-- Better error handling when zero mutated samples are encountered in `clinicalEnrichment`. Issue: [1010](https://github.com/PoisonAlien/maftools/issues/1010)
-- MAJOR: `read.maf` by default coerces clinical data columns to character. This bug fix avoids it and is auto detected. Issue: [997](https://github.com/PoisonAlien/maftools/issues/997)
-
-## ENHANCEMENTS
-- Better handling of color codes for continuous variable annotations [1053](https://github.com/PoisonAlien/maftools/issues/1053)
-- Add `right_mar` to `gisticOncoPlot`[1043](https://github.com/PoisonAlien/maftools/issues/1043)
-- Added `PPDPFL` to protein domain database Issue: [1025](https://github.com/PoisonAlien/maftools/issues/1025)
-- Better sorting of oncoplot with `collapsePathway`
-- Changed default background for oncoplot from `gray` to `#ecf0f1`
-- Changed default signature database to SBS_v3.4 (from legacy)
-- Update `tmb` function
-
-## BREAKING CHNAGES
-- Column order required for `pathways()` function changed from Pathway,Gene to Gene,Pathway. Issue: [1041](https://github.com/PoisonAlien/maftools/issues/1041)
-
-## NEW FUNCTIONS
-- `gisticCompare()` for comparing two GISTIC objects
-- `segSummarize()` for summarizing DNAcopy segments
+- Avoid grid lines crossing over the plotting window in `oncoplot`. Issue: [1069](https://github.com/PoisonAlien/maftools/issues/1069)
+- Fix the title for naming the right bar data. Issue: [1065](https://github.com/PoisonAlien/maftools/issues/1065)
diff --git a/inst/old_news b/inst/old_news
@@ -1,3 +1,31 @@
+# CHANGES IN VERSION 2.22.0
+
+## BUG FIXES
+- Bug fix in using `keepGeneOrder` in `coOncoplot()`. Issue: [1061](https://github.com/PoisonAlien/maftools/issues/1061)
+- Bug fix in using `selectedPathways` in `oncoplot()`. Issue: [1041](https://github.com/PoisonAlien/maftools/issues/1041)
+- Add an error message when bai files are missing `sampleSwaps()`. Issue: [1028](https://github.com/PoisonAlien/maftools/issues/1028)
+- Bug fix in `tmb` while handling multiple MAFs. Issue: [1018](https://github.com/PoisonAlien/maftools/issues/1018)
+- Handle missing `NA`s while sub-setting for ranges. Issue: [1013](https://github.com/PoisonAlien/maftools/issues/1013)
+- Better error handling when zero mutated samples are encountered in `clinicalEnrichment`. Issue: [1010](https://github.com/PoisonAlien/maftools/issues/1010)
+- MAJOR: `read.maf` by default coerces clinical data columns to character. This bug fix avoids it and is auto detected. Issue: [997](https://github.com/PoisonAlien/maftools/issues/997)
+
+## ENHANCEMENTS
+- Better handling of color codes for continuous variable annotations [1053](https://github.com/PoisonAlien/maftools/issues/1053)
+- Add `right_mar` to `gisticOncoPlot`[1043](https://github.com/PoisonAlien/maftools/issues/1043)
+- Added `PPDPFL` to protein domain database Issue: [1025](https://github.com/PoisonAlien/maftools/issues/1025)
+- Better sorting of oncoplot with `collapsePathway`
+- Changed default background for oncoplot from `gray` to `#ecf0f1`
+- Changed default signature database to SBS_v3.4 (from legacy)
+- Update `tmb` function
+
+## BREAKING CHNAGES
+- Column order required for `pathways()` function changed from Pathway,Gene to Gene,Pathway. Issue: [1041](https://github.com/PoisonAlien/maftools/issues/1041)
+
+## 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)