plot.mtDNAaaf: plot.mtDNAaaf function

In mtDNA-BU/mtdnaANNO: Annotation of mtDNA sequence variations

plot.mtDNAaaf function

Description

Produce a Diagnostic Scatter Plot to Visualize AAFs Generated by mtAAF Function

Usage

## S3 method for class 'mtDNAaaf'
plot(x, col = "blue", pch = ".", cex = 0.2, xlab = "", ylab = "", ...)

Arguments

x	a numeric matrix (16569 x N). Rows correspond to loci and columns correspond to subjects. It contains subject ID as the column names, and the AAFs of all 16569 mtDNA loci for each subject. It is generated from mtAAF function.
col	color to be used in the plot.
pch	plotting "character", i.e., symbol to use.
cex	expansion factor for symbols used in the plot.
xlab	a label for the x axis.
ylab	a label for the y axis.
...	arguments to be passed to plot function.

Examples

## Not run: 
## Read input data
allele_file <- "allele.csv"
freq_file   <- "freq.csv"

allele <- as.matrix( read.csv(file=allele_file, sep=",", header=FALSE))
freq   <- as.matrix( read.csv(file=freq_file, sep=",", header=FALSE))

aaf=mtAAF(allele, freq)
plot(aaf)

## End(Not run)

mtDNA-BU/mtdnaANNO documentation built on Aug. 11, 2022, 10:57 a.m.