mutStat {CovidMutations} | R Documentation |
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.
mutStat(
nucmerr = nucmerr,
outdir = NULL,
figure_Type = "TopMuSample",
type_top = 10,
country = FALSE,
mutpos = NULL
)
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 |
Plot the selected figure type as output.
data("nucmerr")
outdir <- tempdir()
mutStat(nucmerr = nucmerr,
outdir = outdir,
figure_Type = "TopCountryMut",
type_top = 10,
country = FALSE,
mutpos = NULL)