globalSNPprofile {CovidMutations}

Global single nucleotide polymorphism (SNP) profiling in virus genome

Description

This function is to visualize the global SNP pattern in the SARS-CoV-2 genome.

Usage

globalSNPprofile(
  nucmerr = nucmerr,
  outdir = NULL,
  figure_Type = "heatmap",
  country = "global",
  top = 5
)

Arguments

nucmerr

Mutation information containing group list(derived from "nucmer" object using "nucmerRMD" function).

outdir

The output directory.

figure_Type

Figure type for either "heatmap" or "count".

country

Choose a country to plot the mutational pattern or choose "global" to profile mutations across all countries. The default is "global".

top

The number of mutational classes to plot.

Value

Plot the selected figure type as output.

Examples

data("nucmerr")
outdir <- tempdir()
globalSNPprofile(nucmerr = nucmerr,
                 outdir = outdir,
                 figure_Type = "heatmap",
                 country = "global",
                 top = 5)