CHANGES IN VERSION 2.0.16
-------------------------
    o Typo fix and added argument `geneOrder` to somaticInteractions. Issue #373
    o Added argument ens2hugo to annovarToMaf. Issue #372
    o Minor bug fix in extractSignatures. Issue #369

CHANGES IN VERSION 2.0.15
-------------------------
    o Bug fix in oncoplot with only 1 variant classification. Issue #367
    o Bug fix with gisticChromPlot. Issue #365
    o Bug fix with plot alignment. Issue #360
    o Update description for lollipopPlot with domain source. Issue #354
    o Optimized method for rank estimation in signature analysis
    o Add barcode_mar and gene_mar to oncoplot and gisticOncoPlot. Issue: #346
    o Add sepwd_genes, sepwd_samples to oncoplot and gisticOncoPlot. Issue: #340 #260
    o Avoid plotting legend outside the margin. Issue: #337
    o Add argument for sample ordering in PlotOncogenicPathways. Issue: #332
    o Add cohortSize argument to oncoplot. Issue: #324
    o coOncoPlot: showing sample names has no effect. Issue: #306

CHANGES IN VERSION 2.0.10
-------------------------
    o Add argument for sample ordering in plotTiTv. Issue: #330
    o Bug fix in annovartomaf which caused wrong annotations for INDLS. Issue: #330

CHANGES IN VERSION 2.0.05
-------------------------
USER-LEVEL IMPROVEMENT
    o merge_mafs - Merge multiple MAF objects, files. Issue: #329
    o Add more examples for oncoplot customization. Issue: #310
    o CoOncoplot - align gene names. Issue: #308
    o Added keepGeneOrder argument to plotVaf. Issue: #305
    o Added sampleOrder argument to gisticOncoPlot. Issue: #302

BUG FIX
    o Fix oncoplot removeNonMutated Error #325
    o SomatinInteractions - Do not ignore samples with no nonsyn variants. Issue: #318
    o Do not convert spaces to underscores while parsing annotations. Issue: #314
    o Fix errors in bubbleplot when the data contains no labels. Issue: #313
    o Fix data.table melt value name in plotVaf. Issue: #311
    o Fix colors for NAs in oncoplot legend. Issue: #309

CHANGES IN VERSION 2.0.0
-------------------------
SIGNIFICANT USER-LEVEL IMPROVEMENT
    o Oncoplot, oncostrip and coOncoplot code has been migrated from ComplexHeatmap to base graphics. Default values for some arguments have been changed.
    o Changed default value for mafObj argument in subsetMaf to TRUE. Issue: #235
    o All ggplots are migrated to base graphics for consistancy
    o TCGA mutations per sample used for tcgaCompare are updated to more stable MC3 cohort from deprecated broad firehose.

IMPROVEMENTS:
    o tcgaCompare now accpets comparing against user specifc cohorts. Issue: #229
    o Add missing genes and samples to oncoplot even when they are not altered. Issue: #254
    o Added MTRNR2L8 protein structure to pfam database. Issue: #255
    o Added addtionalFeature argument to oncoplots. Issue: #270
    o Added log scale option for summary and oncoplots. Issue: #273
    o Made protein domain db compatible with R version < 3.5 Issue: #276
    o Added draw `draw_titv`, and `exprsTbl` argument to oncoplot
    o Additional edits with TMB visualization and additionalFeatures Issue: #289
    o Cooncoplot improvements Issue: #296

BUG FIX
    o Oncoplot annotationOrder bug fix. Issue: #293
    o Update code for AnnovarToMaf. PR #288, #234
    o fixed handling of Status in survival. PR #274
    o Fix swapped confidance intervals in mafCompare function Issue: #269
    o update docs, and vectorized code Issue: #266 #267
    o Improve oncoplot annotations for numeric class Issue: #263 and #203
    o In annovarToMaf read the .tsv file considering the header. PR #259
    o Fix legend title order. Issue: #253
    o GISTIC sample size issue fix. Issue: #249
    o Bug fix for oncoplots with CNV data. Issue: #240
    o Better error handling in plotApobecDiff with no SMGs. Issue: #232
    o Bug fix that caused signature extraction to terminate in case of zero mutations. Issue: #228
    o Bug fix due to missing levels contingency tables in clinical enrichment. Issue: #225
    o Add showTumorSampleBarcodes to PlotOncogenicPathways. Issue: #214
    o Cleanup docs for Oncoplot. Issue: #207
    o Implemented `isNumeric` and `groupAnnotationBySize` to improve sorting. Issue: #207
    o Fix ComplexHeatmap update. Issue: #205 #210
    o plotmafSummary addStats bug fix Issue: #204
    o Rainfall plot data.table null fix. Issue: #201
    o Support non human BSgenome. Issue: #197
    o SampleID bug fix. Issue: #153