regionPlot: regionPlot

In nriddiford/cnvPlotteR: Plotting functions for CNV data

Description

Function to plot a particular region from a single chromosomes for a sample

Usage

regionPlot(cnv_file, from = 2950000, to = 3400000, chrom = "X",
  ylim = c(-5, 5), tick = 1e+05, bp1 = NULL, bp2 = NULL,
  position = NULL, title = NA, ext = "png", theme = "white",
  write = F)

Arguments

cnv_file	File to plot. [Required]
from	Start coordinate of plotting window [Default from=2950000 ]
to	End coordinate of plotting window [Default to=3400000]
chrom	Specify the chromosome to plot [Default 'X']
ylim	Adjust y axis limits in plot [Default ylim=c(-5,5)]
tick	Adjust spacing of ticks [Defualt 1Mb]
bp1	Draw a vertical line at given coordinate to mark bp1
bp2	Draw a vertical line at given coordinate to mark bp2
title	Plot title

Examples

regionPlot(cnv_file="data/w500/test.window-500.cnv", from=3050000, to=3450000, chrom="X", ylim=c(-7,7), bp1=3129368,bp2=3352041, tick=100000, title="222Kb DEL on X")

nriddiford/cnvPlotteR documentation built on Aug. 28, 2020, 5:31 a.m.