plot_snp_density: Title SNP density plot

In JH-Zhou/HandyCNV: HandyCNV: An R package for Standardized Summary, Annotation, Comparison, and Visualization of CNV, CNVR and ROH

Description

Plot SNP density form SNP genotyping map file, the default map file in Plink format. The density will calculate by number of SNPs per Mb.

Usage

plot_snp_density(
  map,
  max_chr = 29,
  top_density = 72,
  low_density = 33,
  color_top = "yellow",
  color_low = "blue",
  color_mid = "red",
  legend_position = c(0.9, 0.1),
  x_label = "Physical distance (Mb)",
  y_label = "Number of SNPs per Mb",
  ncol_1 = 5
)

Arguments

map	Four columns are mandatory in the order of Chr, SNP, CM, Position. No header requires
max_chr	The maximum Chromosome present in SNP density plot. Default value = 29
top_density	Threshold of higher density region, integer number, unit in SNPs/Mb. Default value = 72, suggest setting as the value of Mean + SD of SNP density.
low_density	Threshold of lower density region, integer number, unit in SNPs/Mb. Default value = 33suggest setting as the value of Mean - SD of SNP density.
color_top	Point color of higher density SNPs
color_low	Point color of lower density SNPs
color_mid	Point color of middle regions density SNPS
legend_position	Vectors, default values are c(0.9, 0.1), indicate left bottom corner
x_label	Default label is "Physical distance (Mb)"
y_label	Default label is "Number of SNPs per Mb"
ncol_1	Customize the number of column in final plot, default value is 5.

Value

SNP density plot

JH-Zhou/HandyCNV documentation built on Dec. 18, 2021, 12:25 a.m.