lohView: Construct LOH chromosome plot

In griffithlab/GenVisR: Genomic Visualizations in R

Construct LOH chromosome plot

Description

Given a data frame construct a plot to display Loss of Heterozygosity for specific chromosomes.

Usage

lohView(
  x,
  y = NULL,
  genome = "hg19",
  chr = "chr1",
  ideogram_txtAngle = 45,
  ideogram_txtSize = 5,
  plotLayer = NULL,
  ideogramLayer = NULL,
  out = "plot"
)

Arguments

x	object of class data frame with rows representing Heterozygous Germline calls. The data frame must contain columns with the following names "chromosome", "position", "n_vaf", "t_vaf", "sample".
y	Object of class data frame with rows representing cytogenetic bands for a chromosome. The data frame must contain columns with the following names "chrom", "chromStart", "chromEnd", "name", "gieStain" for plotting the ideogram (optional: see details).
genome	Character string specifying a valid UCSC genome (see details).
chr	Character string specifying which chromosome to plot one of "chr..." or "all"
ideogram_txtAngle	Integer specifying the angle of cytogenetic labels on the ideogram subplot.
ideogram_txtSize	Integer specifying the size of cytogenetic labels on the ideogram subplot.
plotLayer	Valid ggplot2 layer to be added to the copy number plot.
ideogramLayer	Valid ggplot2 layer to be added to the ideogram sub-plot.
out	Character vector specifying the the object to output, one of "data", "grob", or "plot", defaults to "plot" (see returns).

Details

lohView is able to plot in two modes specified via the 'chr' parameter, these modes are single chromosome view in which an ideogram is displayed and genome view where chromosomes are faceted. For the single chromosome view cytogenetic band information is required giving the coordinate, stain, and name of each band. As a convenience GenVisR stores this information for the following genomes "hg19", "hg38", "mm9", "mm10", and "rn5". If the genome assembly supplied to the 'genome' parameter is not one of the 5 afore mentioned genome assemblies GenVisR will attempt to query the UCSC MySQL database to retrieve this information. Alternatively the user can manually supply this information as a data frame to the 'y' parameter, input to the 'y' parameter take precedence of input to 'genome'.

A word of caution, users are advised to only use heterozygous germline calls in input to 'x', failure to do so may result in a misleading visual!

Value

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

Examples

# Plot loh for chromosome 5
lohView(HCC1395_Germline, chr='chr5', genome='hg19', ideogram_txtSize=4)

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