plot.pairwise: Plot values of columns pairwise

In hdng/clonevol: Clonal ordering and visualization

Description

Plot value (eg. VAF) between samples pairwise-ly, annotated and grouped by (eg.) clusters

Usage

## S3 method for class 'pairwise'
plot(data, col.names = c(), suffix = "",
  group.col.name = "cluster", group.col.is.integer = TRUE, colors = NULL,
  shapes = NULL, show.legend.title = FALSE, sharedCategoryColName = "",
  onePage = TRUE, multiPages = FALSE, xMin = 0, xMax = 100, yMin = 0,
  yMax = 100, xMinSmall = 0, xMaxSmall = 70, yMinSmall = 0,
  yMaxSmall = 70, show.none.zero.count = FALSE, out.prefix = "")

Arguments

data	Variant data frames
col.names	The columns to plot all pairwise, eg. VAFs of the samples
suffix	String used to add to col.names as suffix in pairwise plot's axis labels.
group.col.name	The column used to determine the category when plotting to give different shapes,colors. eg. the cluster identity of the variants
onePage	Plot all pairwise plots in a page (default=TRUE)
multiPages	Plot each pairwise plot in a separate page (default=FALSE) of a multi-page PDF output file
xMin, xMax	Min and max values for the x axis in multi-page plots (default=0-100)
yMin, yMax	Min and max values for the y axis in multi-page plots (default=0-100)
xMinSmall, xMaxSmall	Min and max values for the x axis in single-page plot (default=0,70)
yMinSmall, yMaxSmall	Min and max values for the y axis in single-page plot (default=0,70)
out.prefix	Output files' prefix

Examples

data(aml1)
plot.pairwise(aml1$variants, col.names = aml1$params$vaf.col.names,
              out.prefix = 'variants.pairwise.plot')

hdng/clonevol documentation built on May 17, 2019, 3:19 p.m.