plotPCA {psichomics}R Documentation

Create a scatterplot from a PCA object

Description

Create a scatterplot from a PCA object

Usage

plotPCA(pca, pcX = 1, pcY = 2, groups = NULL, individuals = TRUE,
  loadings = FALSE, nLoadings = NULL)

Arguments

pca

prcomp object

pcX

Character: name of the X axis of interest from the PCA

pcY

Character: name of the Y axis of interest from the PCA

groups

Matrix: groups to plot indicating the index of interest of the samples (use clinical or sample groups)

individuals

Boolean: plot PCA individuals

loadings

Boolean: plot PCA loadings/rotations

nLoadings

Integer: Number of variables to plot, ordered by those that most contribute to selected principal components (this allows for faster performance as only the most contributing variables are rendered); if NULL, all variables are plotted

Value

Scatterplot as an highchart object

Examples

pca <- prcomp(USArrests, scale=TRUE)
plotPCA(pca)
plotPCA(pca, pcX=2, pcY=3)

# Plot both individuals and loadings
plotPCA(pca, pcX=2, pcY=3, loadings=TRUE)

[Package psichomics version 1.10.1 Index]