pcadapt (version 2.2)

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 available : "screeplot", "scores", "stat.distribution", "manhattan" and "qqplot". "screeplot" shows the decay of the singular values of the genotype matrix 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 principal component of interest. "qqplot" draws a Q-Q plot of the p-values associated with the principal component of interest.

Usage

## S3 method for class 'pcadapt':
plot(x, ..., option = NULL, K = NULL, i = 1, j = 2,
  pop = attr(x, "pop"), subcol = NULL, threshold = NULL, num_pc = 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 lists of indices specifying the subpopulations. This attributes specific colors to each subpopulations.

subcol

a list of colors for each subpopulation. If not specified, default colors will be used.

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.

num_pc

an integer specifying the number of components to take into account in the scree plot. num_axis should be lower than K. By default, num_axis = K.

Examples

## see ?pcadapt for examples