globalProteinMut {CovidMutations}

Global mutational events profiling of proteins

Description

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

Usage

globalProteinMut(
  covid_annot = covid_annot,
  outdir = NULL,
  figure_Type = "heatmap",
  top = 10,
  country = "global"
)

Arguments

covid_annot

The mutation effects provided by "indelSNP" function.

outdir

The output directory.

figure_Type

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

top

The number of variants to plot.

country

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

Value

Plot the selected figure type as output.

Examples

data("covid_annot")
outdir <- tempdir()
# make sure the covid_annot is a dataframe
covid_annot <- as.data.frame(covid_annot)
globalProteinMut(covid_annot = covid_annot,
                 outdir = outdir,
                 figure_Type = "heatmap",
                 top = 10,
                 country = "USA")