## CHANGES IN VERSION 2.2.10
### BUG FIX
    o Avoid in place class conversion for data.frames Issue: #432
    o Fix vignette entry Issue: #442

### ENHANCEMENTS
    o Improvised estimateSignatures function Issue: #433
    o Added clinQuery argument to `subsetMaf` function Issue: #423
    o Improvised somaticInteractions. Better plot and displays counts Issue: #418, #420


## CHANGES IN VERSION 2.2.0
### NEW FUNCTIONS AND FEATURES
    o `survGroup`, `mafSurvGroup` - Predict genes/genesets associated with survival. Issue: #396
    o New argument `altered` in `oncoplot` to plot top genes based on CNV or mutation. Default is `FALSE`. Issue: #405

### DEPRECATED
    o `oncotate` - Oncotator is no longer supported by Broad. Issue: #403 #384 #381
    o `findPathways` argument in `somaticInteractions` function has been deprecated

### SIGNIFICANT USER-LEVEL IMPROVEMENT
    o Signature analysis has been modified to be more flexible. It now consits of three functions namely:
        o `estimateSignatures` - which measures cophenetic correlation metric (a measure of goodness of fit) for a range of values
        o `plotCophenetic` - which draws an elbow plot of cophenetic correlation metric from `estimateSignatures` and helps to decide an optimal number of signature `(n)`.
        o `extractSignatures` - which then extracts final `n` signatures
    o `compareSignatures` now has two databases of known signatures. Classic 30 signatures and newer 67 SBS signatures from COSMIC.

### BUG FIX
    o `gisticChromPlot` bug fix. Issue: #392
    o `annovarToMaf` bug fix for results without exonic variants. Issue: #388
    o Avoid conflict with `plotly::layout` with `graphcis::layout`. Issue: #387 #202
    o Fix side-bar heights in Oncoplot with copy-number data. Issue: #383
    o Update y-axis label for `tcgaCompare` plot. Issue: #366
    o `annovarToMaf` annotating variants with MNPs. Issue: #335

CHANGES IN VERSION 2.0.16
-------------------------
    o Minor bug fix in extractSignatures. Issue #369
    o Added argument ens2hugo to annovarToMaf. Issue #372

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

BUG FIX
    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

CHANGES IN VERSION 1.8.0
-------------------------
NEW FUNCTIONS
    o OncogenicPathways - Perform enrichment for known oncogenic pathways from TCGA studies.
    o PlotOncogenicPathways - Plots OncogenicPathways results
    o drugInteractions - Drug gene interactions from DGIB database.

SIGNIFICANT USER-LEVEL IMPROVEMENT
    o trinucleotideMatrix functions now works with BSgenomes instead of time consuming fasta files
    o rainfallPlot now detects Kataegis based on a greedy algorithm

CHANGES IN VERSION 1.6.15
-------------------------
BUG FIX
    o somaticInteractions data.table fix. Issue: #166
    o Fixed error due to multiple header lines from TCGA MAF files. Issue: #162
    o APOBEC enrichment estimation, context fix. Issue: #160
ENHANCEMENTS:
    o Update warning and error messages. Issue: #181, #178
    o Added argument dropLevels to subsetMaf. Issue: #186
    o Added argument sortByAnnotation1 to coOncoplot for sorting by clinical annotation. Issue: #168
    o Added argument colbar_pathway to oncoplot for controlling mutation burden display. Issue: #167, #169
    o Fixed showBarcodes in plotmafSummary. Summary plot now includes annotations (% or raw number) on the barplot. Issue: #165
    o Added argument bgCol and borderCol to oncoplots for better background representation. Issue: #164

CHANGES IN VERSION 1.6.10
-------------------------
BUG FIX
    o APOBEC enrichment estimation, denominator fix. Issue: #160
    o Total sample estimation bug fix. Issue: #159
    o fix plot error caused by NAs in signatureEnrichment. PR: #158

CHANGES IN VERSION 1.6.07
-------------------------
BUG FIX
    o Correct ordering of mutsigCV q-values in oncoplot. Issue: #144
    o Bioconductor windows error fix

CHANGES IN VERSION 1.6.05
-------------------------
BUG FIX
    o Fix breaks due to changes in data.table 1.11.0. Issue: #143
    o SomaticInteraction bug fix due to hclust. Issue: #142

CHANGES IN VERSION 1.6.00
-------------------------
NEW FUNCTIONS
    o clinicalEnrichment - Performs mutational enrichment analysis for a given clinical feature.
    o signatureEnrichment - Performs sample stratification based on signature exposures and enrichment analysis.
    o plotEnrichmentResults - Plots results from clinicalEnrichment and signatureEnrichment analysis
    o lollipopPlot2 - Compare two lollipop plots

SIGNIFICANT USER-LEVEL IMPROVEMENT
    o Forstplot now includes summary table within the plot.
    o Included capture_size argument in tcgaCompare.
    o annovarToMaf can take multiple annovar annotation files and converts them to a single MAF cohort.
