visPMSignature: Visualize estimated probabilistic mutation signatures

In friend1ws/pmsignature: Extracting characteristic mutation signatures from a set of mutation data.

Description

By checking the meta-information on the mutation signature (model type, #flanking-bases, transcription strand usages), appropriate visualization will be automatically produced (but currently, we are supporting just for "independent" and "full" type models).

Usage

visPMSignature(object, sinInd = 1, ...)

Arguments

object	EstimatedParameters class
sigInd	the index of the mutation signature plotted
baseCol	the colors of the bases (A, C, G, T, plus strand, minus strand), (default: ggplot2 default colors, active only if type = "independent")
charSize	the size of the character passed to geom_text function (default: 5 (active only if type = "independent")
isScale	the index whether the height of the flanking base is changed or not (default: FALSE, active only if type = "independent")
alpha	the parameter for the Renyi entropy (default: 2, applicable only if the isScale == TRUE)

Value

a figure of estimated probabilistic mutation signature via ggplot2 is generated (therefore, can be saved using ggsave function).

Examples

After obtaining EstimatedParameters (typically by \code{getPMSignature}) as Param,
visPMSignature(Param, 1)

You can change the heights of flanking bases according to information contents,
visPMSignature(Param, 1, isScale = TRUE)

friend1ws/pmsignature documentation built on May 16, 2019, 3:27 p.m.