plotFeatureBoundaryCoverage {RCAS} | R Documentation |
This function is used to create interactive plots displaying 5' and 3' end coverage profiles of given transcript features.
plotFeatureBoundaryCoverage(cvgF, cvgT, featureName)
cvgF |
data.frame object containing 'fiveprime' coverage data returned by getFeatureBoundaryCoverage function |
cvgT |
data.fram object containing 'threeprime' coverage data returned by getFeatureBoundaryCoverage function |
featureName |
character object. This is used to label the axes (e.g. transcripts, exons) |
a plotly htmlwidget is returned
data(queryRegions) data(gff) txdb <- GenomicFeatures::makeTxDbFromGRanges(gff) transcriptCoords <- GenomicFeatures::transcripts(txdb) cvgF <- getFeatureBoundaryCoverage (queryRegions = queryRegions, featureCoords = transcriptCoords, flankSize = 100, boundaryType = 'fiveprime', sampleN = 1000) cvgT <- getFeatureBoundaryCoverage (queryRegions = queryRegions, featureCoords = transcriptCoords, flankSize = 100, boundaryType = 'threeprime', sampleN = 1000) p <- plotFeatureBoundaryCoverage(cvgF = cvgF, cvgT = cvgT, featureName = 'transcript')