cnFreq: Construct copy-number frequency plot

In griffithlab/GenVisR: Genomic Visualizations in R

Construct copy-number frequency plot

Description

Given a data frame construct a plot to display copy number changes across the genome for a group of samples.

Usage

cnFreq(
  x,
  CN_low_cutoff = 1.5,
  CN_high_cutoff = 2.5,
  plot_title = NULL,
  CN_Loss_colour = "#002EB8",
  CN_Gain_colour = "#A30000",
  x_title_size = 12,
  y_title_size = 12,
  facet_lab_size = 10,
  plotLayer = NULL,
  plotType = "proportion",
  genome = "hg19",
  plotChr = NULL,
  out = "plot"
)

Arguments

x	Object of class data frame with rows representing genomic segments. The data frame must contain columns with the following names "chromosome", "start", "end", "segmean", and "sample". Coordinates should be 1-based space.
CN_low_cutoff	Numeric value representing the point at or below which copy number alterations are considered losses. Only used if x represents CN values.
CN_high_cutoff	Numeric value representing the point at or above which copy number alterations are considered gains. Only used if x represents CN values.
plot_title	Character string specifying the title to display on the plot.
CN_Loss_colour	Character string specifying the colour value for copy number losses.
CN_Gain_colour	Character string specifying the colour value for copy number gains.
x_title_size	Integer specifying the size of the x-axis title.
y_title_size	Integer specifying the size of the y-axis title.
facet_lab_size	Integer specifying the size of the faceted labels plotted.
plotLayer	Valid ggplot2 layer to be added to the plot.
plotType	Character string specifying the type of values to plot. One of "proportion" or "frequency"
genome	Character string specifying a valid UCSC genome (see details).
plotChr	Character vector specifying specific chromosomes to plot, if NULL all chromosomes for the genome selected are displayed.
out	Character vector specifying the the object to output, one of "data", "grob", or "plot", defaults to "plot" (see returns).

Details

cnFreq requires the location of chromosome boundaries for a given genome assembly in order to ensure the entire chromosome space is plotted. As a convenience this information is available to cnSpec for the following genomes "hg19", "hg38", "mm9", "mm10", "rn5" and can be retrieved by supplying one of the afore mentioned assemblies via the 'genome' parameter. If a genome assembly is supplied to the 'genome' parameter and is unrecognized cnSpec will attempt to query the UCSC MySQL database for the required information. If genomic segments are not identical across all samples the algorithm will attempt to perform a disjoin operation splitting existing segments such that there are no overlaps. The 'plotLayer' parameter can be used to add an additional layer to the ggplot2 graphic (see vignette).

Value

One of the following, a dataframe containing data to be plotted, a grob object, or a plot.

Examples

# plot on internal GenVisR dataset
cnFreq(LucCNseg)

griffithlab/GenVisR documentation built on May 14, 2024, 12:40 a.m.