ezpca: PCA plot of top two components

In jdreyf/ezlimmaplot: Bioinformatics plots using limma and ggplot2, some from output of ezlimma

PCA plot of top two components

Description

PCA plot of top two principal components using ggplot2.

Usage

ezpca(
  object,
  pheno.df = NULL,
  name = "pca",
  alpha = 1,
  all.size = NULL,
  facet = NULL,
  title = NULL,
  subtitle = NULL,
  rm.leg.title = FALSE,
  labels = FALSE,
  manual.color = NULL,
  manual.shape = NULL,
  ellipses = FALSE,
  plot = TRUE,
  ...
)

Arguments

object	Matrix-like object with features (e.g. genes) as rows and samples as columns.
pheno.df	Data frame with rows as samples and columns as phenotypes.
name	Name of file to create. Set to NA to plot to screen instead of to file.
alpha	Transparency, passed to geom_point.
all.size	Passed to geom_point size parameter to give size for all points without appearing in legend. ggplot2 default is size=2.
facet	A formula with columns in pheno.df to facet by.
title	Title text; suppressed if it is NULL.
subtitle	Subtitle text; suppressed if it is NULL or title is NULL. If you'd like a subtitle but no title, set title = "".
rm.leg.title	Logical indicating if legend title should be removed.
labels	Logical, should sample labels be added next to points?
manual.color	Vector passed to scale_colour_manual for creating a discrete color scale. Vector length should be equal to number of levels in mapped variable.
manual.shape	Vector passed to scale_shape_manual for creating a discrete color scale. Vector length should be equal to number of levels in mapped variable.
ellipses	Logical; should probability ellipses be drawn?
plot	Logical; should plot be generated?
...	Passed to aes_string.

Details

PCA is calculated with prcomp. object must have colnames, and if pheno.df is given, it is checked that colnames(object)==rownames(pheno.df).

Value

Invisibly, a ggplot object. Its data element contains the first two principal components appended to pheno.df.

jdreyf/ezlimmaplot documentation built on Feb. 8, 2025, 2:25 a.m.