bexy (version 0.1.3)

plotCounts: Plotting the percentage of counts mapping to two scaffolds (by default a Y-linked scaffold against a X-linked scaffold), colored by sex karyotype

Description

Plotting the percentage of counts mapping to two scaffolds (by default a Y-linked scaffold against a X-linked scaffold), colored by sex karyotype

Usage

plotCounts(
  x,
  scaffoldX = NULL,
  scaffoldY = NULL,
  colors = c("turquoise3", "darkorange", "royalblue4"),
  sampleNamesToHighlight = c(),
  label = TRUE,
  ...
)

Value

No return value, called for side effects.

Arguments

x

A bexy object.

scaffoldX

A string with the name of the scaffold to be plotted on the x-axis. If NULL (default), a X-linked scaffold is used.

scaffoldY

A string with the name of the scaffold to be plotted on the y-axis. If NULL (default), a Y-linked scaffold is used.

colors

A vector of length three with the colors for aneuploid, XX and XY samples, respectively.

sampleNamesToHighlight

A vector of sample names that should be highlighted. If empty, samples are automatically highlighted based on the posterior probabilities.

label

Boolean indicating whether samples should be labeled.

...

Other parameters used for plotting.

See Also

bexy

Examples

bex <- bexy()
plotCounts(bex)