Changes in version 2.4.12                        

BUG FIXES

  - Fix issue reversed colors in somaticInteractions. Setting
    limitColorBreaks = TRUE by default for the fix. Issue: 589
  - Fix issue with non-numeiric error in math.score. Issue: 429
  - Fix issue with zcat for file names with spaces. Let data.table deal
    with it. Issue: 574
  - Fix margins in tcgaCompare. Issue: 573
  - Fix labels in somaticInteractions. Issue: 569
  - Clinical features with same labels are colored similarly in
    Oncoplot. Issue: 567
  - Legend Ordering Not Intuitive. Issue: 424
  - avoid in place conversions of data.frames while reading with
    read.maf. Issue: 432 593

ENHANCEMENTS

  - Added bands argument to gisticOncoPlot. Issue: 579
  - Added ranges argument to subsetMaf. Issue: 571
  - Added barcodeSrt, annoBorderCol arguments to oncoplot. Issue: 564
    565
  - Added minMut argument to oncoplot. Issue: 549

                       Changes in version 2.4.05                        

BUG FIXES

  - Bugfix in annotation legend order in oncoplot. Issue: 541
  - Error in plotCBSsegments. Issue: 539
  - merge_mafs bug fix due to discrepancy in column names. Issue: 538
  - readGistic TCGA sample names bug fix. Issue: 536
  - Highlight most significant entry when a variants overlaps with
    multiple CNV regions Issue: 524
  - genesToBarcodes sample selection fix
  - coOncoplot bug fix with showSampleNames argument. Issue: 306
  - removeNonMutated bug fix with oncoplot argument. Issue: 530

ENHANCEMENTS

  - Make flags internal function with top 100 genes. Issue: 542
  - Add legend to gisticBubblePlot. Issue: 544
  - Add bgCol and borderCol to gisticOncoPlot. Issue: #533
  - Allow multiple CN types in oncoplot Issue: #490
  - Allow getSampleSummary to include non mutated samples Issue: #527
  - Added color argument to plotVaf for manual color codes Issue: #531
  - Added rm_zero argument to tcgaCompare

                       Changes in version 2.4.00                        

BUG FIXES

  - lollipopPlot2 error with zero mutation Issue: #480
  - inferHeterogeneity PR #473
  - oncoplot cnv crosses border #472
  - Avoid wrongly naming columns in annovarToMaf Issue: #457
  - Duplicated color code Issue: #452
  - oncoplot with exprsTbl leads to wrong alignment Issue: #451
  - plotMafSummary with single sample Issue: #449
  - Avoid empty spaces and quoates while reading funcotator MAF Issue:
    #403 #397

ENHANCEMENTS

  - OncogenicPathways improvements Issue: #505
  - Added showSum, colNC, nShiftSymbols, sigSymbolsSize,
    sigSymbolsFontSize, pvSymbols arguments to somaticInteractions PR:
    #505 Thanks zmiimz
  - Added anno_height, drawBox, drawExtraBar arguments to oncoplot PR:
    #501 Thanks Kai Gu
  - Added decreasing argument to tcgaComapre Issue: #497
  - Added startgain and startlost to annovarToMaf Issue: #487
  - y_lims argument in gisticChromPlot Issue: #485
  - Added support for highlighting multiple additionalFeatures Issue:
    #476
  - Pairwise t-test and mutational load in tcgaCompare Issue: #453
  - Added titleText argument to oncoplot Issue: #448
  - Highlight mutated genes on gisticChromplot Issue: #443
  - Added legend_height argument to oncoplot Issue: #346
  - Added bgBorderCol domainBorderCol showLegend argument to
    lollipopPlot

NEW FUNCTIONS AND FEATURES

  - tmb Simple tumor mutation burden estimation function.
  - setdiffMAF and intersectMAF. Set operations for MAF files. PR: #508
    Thanks Shixiang Wang
  - tcgaDriverBP Compare genes to known TCGA drivers and their
    biological pathways
  - vafCompare plots vaf distribution of target genes from two cohorts
    Issue: #495
  - coBarplot side-by-side barplot for maf comparison Issue: #486
  - Group genes in oncoplot by specific pathways. This can be done by
    setting pathways = 'auto' or by providing a two column
    data.frame/tsv-file with Gene names and their corresponding pathway
    belongings.
  - Oncoplot gains rightBarData and leftBarData arguments for user
    specific side bar plots.
  - Default flatUI colors for lollipop plots

Deprecated

  - geneCloud and pancanComparison