CovidMutations (version 0.1.3)

mutStat: Plot mutation statistics for nucleiotide

Description

Visualization for the top mutated samples, average mutational counts, top mutated position in the genome, mutational density across the genome and distribution of mutations across countries.

Usage

mutStat(
  nucmerr = nucmerr,
  outdir = NULL,
  figure_Type = "TopMuSample",
  type_top = 10,
  country = FALSE,
  mutpos = NULL
)

Arguments

nucmerr

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

outdir

The output directory.

figure_Type

Figure type for: "TopMuSample", "AverageMu", "TopMuPos", "MutDens", "CountryMutCount", "TopCountryMut".

type_top

To plot the figure involving "top n"("TopMuSample", "TopMuPos", "TopCountryMut"), the "type_top" should specify the number of objects to display.

country

To plot the figure using country as groups("CountryMutCount" and "TopCountryMut"), the "country" should be TRUE.

mutpos

If the figure type is "TopCountryMut", "mutpos" can specify A range of genomic position(eg. 28831:28931) for plot

Value

Plot the selected figure type as output.

Examples

# NOT RUN {
data("nucmerr")
outdir <- tempdir()
mutStat(nucmerr = nucmerr,
        outdir = outdir,
        figure_Type = "TopCountryMut",
        type_top = 10,
        country = FALSE,
        mutpos = NULL)
# }