cnView_buildMain {GenVisR}R Documentation

construct CN plot

Description

given a CN data frame plot points in ggplot

Usage

cnView_buildMain(x, y, z = NULL, chr, CNscale = FALSE, layers = NULL,
  segmentColor = NULL)

Arguments

x

a data frame with columns chromosome, coordinate, cn, p_value

y

a data frame with columns chromosome, coordinate for plotting boundaries

z

a data frame with columns chromsome, start, end, segmean specifying segments called from copy number (optional)

chr

a character string specifying chromosome

CNscale

Character string specifying if copy number calls supplied are relative (i.e.copy neutral == 0) or absolute (i.e. copy neutral ==2). One of "relative" or "absolute"

layers

additional ggplot2 layers to add

segmentColor

Character string specifying the color of segment lines. Used only if Z is not null.

Value

ggplot2 object


[Package GenVisR version 1.8.1 Index]