PCA_plot: Create a PCA plot

In omu: A Metabolomics Analysis Tool for Intuitive Figures and Convenient Metadata Collection

Create a PCA plot

Description

Performs an ordination and outputs a PCA plot using a metabolomics count data frame and metabolomics metadata

Usage

PCA_plot(
  count_data,
  metadata,
  variable,
  color,
  response_variable = "Metabolite",
  label = FALSE,
  size = 2,
  ellipse = FALSE
)

Arguments

count_data	Metabolomics count data
metadata	Metabolomics metadata
variable	The independent variable you wish to compare and contrast
color	String of what you want to color by. Usually should be the same as variable.
response_variable	String of the response_variable, usually should be "Metabolite"
label	TRUE or FALSE, whether to add point labels or not
size	An integer for point size.
ellipse	TRUE or FALSE, whether to add confidence interval ellipses or not.

Examples

PCA_plot(count_data = c57_nos2KO_mouse_countDF, metadata = c57_nos2KO_mouse_metadata,
variable = "Treatment", color = "Treatment", response_variable = "Metabolite")

omu documentation built on Oct. 17, 2023, 1:06 a.m.