clonevol (version 0.99.11)

plot.pairwise: Plot values of columns pairwise

Description

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

Usage

# S3 method for 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

# NOT RUN {
data(aml1)
plot.pairwise(aml1$variants, col.names = aml1$params$vaf.col.names,
              out.prefix = 'variants.pairwise.plot')

# }