get_oncoplots {ProgModule} | R Documentation |
Draw a waterfall plot of mutated genes involved in the module
Description
Load the data in MAF format and draws a waterfall plot of mutated genes involved in the module.
Usage
get_oncoplots(
maf,
genes,
removeNonMutated = TRUE,
top = 20,
minMut = NULL,
altered = FALSE,
drawRowBar = TRUE,
drawColBar = TRUE,
leftBarData = NULL,
leftBarLims = NULL,
rightBarData = NULL,
rightBarLims = NULL,
topBarData = NULL,
logColBar = FALSE,
includeColBarCN = TRUE,
clinicalFeatures = NULL,
annotationColor = NULL,
annotationDat = NULL,
pathways = NULL,
path_order = NULL,
selectedPathways = NULL,
pwLineCol = "#535c68",
pwLineWd = 1,
draw_titv = FALSE,
titv_col = NULL,
showTumorSampleBarcodes = FALSE,
barcode_mar = 4,
barcodeSrt = 90,
gene_mar = 5,
anno_height = 1,
legend_height = 4,
sortByAnnotation = FALSE,
groupAnnotationBySize = TRUE,
annotationOrder = NULL,
sortByMutation = FALSE,
keepGeneOrder = FALSE,
GeneOrderSort = TRUE,
sampleOrder = NULL,
additionalFeature = NULL,
additionalFeaturePch = 20,
additionalFeatureCol = "gray70",
additionalFeatureCex = 0.9,
genesToIgnore = NULL,
fill = TRUE,
cohortSize = NULL,
colors = NULL,
cBioPortal = FALSE,
bgCol = "#CCCCCC",
borderCol = "white",
annoBorderCol = NA,
numericAnnoCol = NULL,
drawBox = FALSE,
fontSize = 0.8,
SampleNamefontSize = 1,
titleFontSize = 1.5,
legendFontSize = 1.2,
annotationFontSize = 1.2,
sepwd_genes = 0.5,
sepwd_samples = 0.25,
writeMatrix = FALSE,
colbar_pathway = FALSE,
showTitle = TRUE,
titleText = NULL,
showPct = TRUE
)
Arguments
maf |
The patients' somatic mutation data, which in MAF format. |
genes |
Modular gene set from final_candidate_module,generated by 'get_final_candidate_module'. |
removeNonMutated , top , minMut , altered , drawRowBar , drawColBar , leftBarData , leftBarLims , rightBarData , rightBarLims , topBarData , logColBar , includeColBarCN , clinicalFeatures , annotationColor , annotationDat , pathways , path_order , selectedPathways , pwLineCol , pwLineWd , draw_titv , titv_col , showTumorSampleBarcodes , barcode_mar , barcodeSrt , gene_mar , anno_height , legend_height , sortByAnnotation , groupAnnotationBySize , annotationOrder , sortByMutation , keepGeneOrder , GeneOrderSort , sampleOrder , additionalFeature , additionalFeaturePch , additionalFeatureCol , additionalFeatureCex , genesToIgnore , fill , cohortSize , colors , cBioPortal , bgCol , borderCol , annoBorderCol , numericAnnoCol , drawBox , fontSize , SampleNamefontSize , titleFontSize , legendFontSize , annotationFontSize , sepwd_genes , sepwd_samples , writeMatrix , colbar_pathway , showTitle , titleText , showPct |
see |
Value
No return value
Examples
#load the data.
maffile<-system.file("extdata","maffile.maf",package="ProgModule")
data(final_candidate_module)
#draw an oncoplot
get_oncoplots(maf=maffile,genes=final_candidate_module[[1]])
[Package ProgModule version 0.1.0 Index]