omu (version 1.1.2)

PCA_plot: 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")