NEWS

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maftools 2.18.0

NEW FUNCTIONS

• pathways and plotPathwaysfor summarizing & visualizing pathways Issue: 956
• coGisticChromPlot for plotting two GISTIC objects side-by-side. PR by biosunsci 954
• readGistic can take gistic output directory as an input. PR by biosunsci 954

BUG FIXES

• Bug fixes while processing custom pathways
• Bug fix in oncoplot for drawing borders. 958
• Bug fix in plotSignatures for hardcoded axis limits. 949
• Bug fix in mafSurvival legend when samples argument is give. 937
• Bug fix in subsetMaf while handling only CNV events. 908
• Error handling when no deep/shallow CNV events found. 899
• Bug fix in oncoplot for duplicated values in gene list. 889

ENHANCEMENTS

• Added argument collapsePathway to oncoplot. Issue: 956
• Improved annovarToMaf with better handling of indels and Variant_Type. Issue: 940
• Include absolute contribution of each signature in extractSignatures output. Issue: 939
• Added tsbToPIDs for custom names in oncoplot. Issue: Issue: 936
• Added DSEL protein to the database. Issue: 933
• Added MUC3A protein to the database. Issue: 932
• Added showOnlyPathway argument to oncoplot
• Added pathdb argument to PlotOncogenicPathways. Issue: 923
• Emit warnings when fishers test can not be performed during somaticInteractions. Issue: 921
• Added leftMar and topMar arguments to somaticInteractions. Issue: 913
• Added toptBarLims argument to oncoplot. Issue: 910
• Added data argument to lollipopPlot function. Issue: 894
• Added sortByM1 and sortByM2 argument to coOncoplot. Issue: 888
• Added arguments leftBarVline, leftBarVlineCol, rightBarVline, rightBarVlineCol topBarHline topBarHlineCol to oncoplot. Issue: 874
• Added revPal argument to somaticInteractions. Issue: 859
• Fix legend and color codes for numeric annotations in oncoplot. Issue: 363