PCA plot from counts matrix

Usage

PCAplot(
  object,
  use.pc = c(1, 2),
  color = NULL,
  label = NULL,
  shape = NULL,
  title = NULL,
  vst.norm = FALSE,
  palette = NULL,
  repel = TRUE
)

Arguments

object: A count matrix.
use.pc: Which two PCs to be used, default PC1 in x-axis and PC2 in y-axis.
color: Vector indicates the color mapping of samples, default NULL.
label: Vector of sample names or labels, default NULL.
shape: Vector indicates the shape mapping of samples, default NULL.
title: Plot title, default NULL.
vst.norm: Whether to perform vst transformation, default FALSE.
palette: The color palette for different groups.
repel: Whether to use ggrepel to avoid overlapping text labels or not, default TRUE.

Value

ggplot2 object

Details

Perform PCA based on matrix using prcomp, and visualized with scatter plot.