visMembership: Visualize estimated membership parameters

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

Description

Visualize estimated membership parameters

Usage

visMembership(object1, object2, ylog = FALSE, sortSampleNum = TRUE,
  multiplySampleNum = TRUE, fromSample = NULL, toSample = NULL,
  reorderSig = NULL, colourBrewer = NULL)

Arguments

object1	MutationFeatureData class
object2	EstimatedParameters class
ylog	barplot height is an logarithms of #mutations or not (default: FALSE, active only if multiplySampleNum = TRUE).
sortSampleNum	samples are sorted according to #mutations (default: TRUE).
multiplySampleNum	barplot height for each sample is multiplied by #mutations (default: TRUE).
fromSample	only samples from the specified index will be plotted (default: NULL).
reorderSig	the order of signatures are reordered according to the specified order (default: NULL).
colourBrewer	colourBrewer palette set passed to scale_fill_brewer function. See, e.g., http://docs.ggplot2.org/current/scale_brewer.html for detail.
fromSample	only samples until the specified index will be plotted (default: NULL).

Value

a figure of estimated membership parameter via ggplot2 is generated (therefore, can be saved using ggsave function).

Examples

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

You can equate the heights of barplot
visPMSignature(G,Param, multiplySampleNum = TRUE)

Use colourBrewer palette,
visPMSignature(G,Param, colourBrewer = "Set2")

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