ShowSNPDensityPlot {handyFunctions}

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))