ShowSNPDensityPlot: Function of showing SNP density at chromosome level

In handyFunctions: Useful Functions for Handfully Manipulating and Analyzing Data with Data.frame Format

Function of showing SNP density at chromosome level

Description

Function of showing SNP density at chromosome level

Usage

ShowSNPDensityPlot(
  densityData,
  binSize,
  densityColorBar = c("grey", "darkgreen", "yellow", "red"),
  chromSet = c(1:22),
  withchr = FALSE
)

Arguments

densityData	the raw density data generated from vcftools
binSize	the bin size set while generating density data
densityColorBar	vector Specific the color bar for plotting density plot (generally four colors)
chromSet	vector Filtered chrom set which you want to plot (it must be matched with the CHROM column in densityData)
withchr	logical If the chromsome labels of density plot is prefixed with "chr". Note: it cannot work when the filtered chrom set contain other uncommon chrom symbols (e.g. NC0*, etc)

Value

A ggplot2 object for SNP density plot

Examples

library(handyFunctions)
data(SNV_1MB_density_data)
ShowSNPDensityPlot(SNV_1MB_density_data, binSize = 1e6, chromSet = c(38:1))

handyFunctions documentation built on Aug. 22, 2022, 5:06 p.m.