cnSpec_buildMain {GenVisR}R Documentation

Construct CN cohort plot

Description

given a data frame construct a plot to display CN information for a group of samples

Usage

cnSpec_buildMain(data_frame, dummy_data, plot_title = NULL,
  CN_low_colour = "#002EB8", CN_high_colour = "#A30000", x_lab_size = 12,
  y_lab_size = 12, facet_lab_size = 10, layers = NULL,
  CNscale = "absolute")

Arguments

data_frame

object of class data frame containing columns chromosome, start, end, cn, sample

dummy_data

Object of class data frame containing columns chromosome, start, end, cn, sample. Used for defining chromosome boundaries

plot_title

character string for title of plot

CN_low_colour

character string specifying low value of colour gradient

CN_high_colour

character string specifying high value of colour gradient

x_lab_size

integer specifying the size of the X label

y_lab_size

integer specifying the size of the Y label

facet_lab_size

integer specifying the size of the faceted labels

layers

Additional layers to be plotted, can be a theme but must be a ggplot layer

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"

Value

ggplot object


[Package GenVisR version 1.8.1 Index]