pcadapt (version 3.0)

plot.pcadapt: pcadapt visualization tool

Description

plot.pcadapt is a method designed for objects of class pcadapt. It provides a plotting utile for quick visualization of a pcadapt object. Different options are currently available : "screeplot", "scores", "stat.distribution", "manhattan" and "qqplot". "screeplot" shows the decay of the genotype matrix singular values and provides a figure to guide in the choice of K. "scores" plots the projection of the individuals onto the first two principal components. "stat.distribution" displays the histogram of the selected test statistics, as well as the estimated distribution for the neutral SNPs. "manhattan" draws the Manhattan plot of the p-values associated with the statistic of interest. "qqplot" draws a Q-Q plot of the p-values associated with the statistic of interest.

Usage

## S3 method for class 'pcadapt':
plot(x, ..., option = "manhattan", K = NULL, i = 1,
  j = 2, pop, threshold = NULL)

Arguments

x

an object of class "pcadapt" generated with pcadapt.

...

...

option

a character string specifying the figures to be displayed. If NULL (the default), all three plots are printed.

K

an integer specifying the principal component of interest. K has to be specified only when using the loadings option.

i

an integer indicating onto which principal component the individuals are projected when the "scores" option is chosen. Default value is set to 1.

j

an integer indicating onto which principal component the individuals are projected when the "scores" option is chosen. Default value is set to 2.

pop

a list of integers or strings specifying which subpopulation the individuals belong to.

threshold

for the "qqplot" option, it displays an additional bar which shows the threshold percent of SNPs with smallest p-valuesseparates the SNPs with the highest p-values.

Examples

## see ?pcadapt for examples