Skip to contents

Plot PCA

PlotPCA.Rd

PCA scatter plot with blanks and QC pool observations marked with a border

Usage

PlotPCA(
  pca,
  x = "PC1",
  y = "PC2",
  colorBy = "Group",
  pointSize = 3,
  pointAlpha = 0.8,
  interactive = FALSE
)

Arguments

pca

The PCA and variance explained data from GetPCA()

x, y

The principal components (prefixed with "PC") to plot on the X and Y axes

colorBy

The column by which to color the points (using aes(fill = ...))

pointSize

The size of the ggplot2::geom_point()

pointAlpha

The transparency of the ggplot2::geom_point()

interactive

Whether to plot as interactive with ggiraph::geom_point_interactive()

Value

A named list where pca is the PCA data column bound to fullData and varex which contains the percent variance explained for each PC.