plotPCA: Principle Component Analysis plot

In jasenfinch/metabolyseR: Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabolomics Data

Principle Component Analysis plot

Description

Plot Principle Component Analysis results.

Usage

plotPCA(
  analysis,
  cls = "class",
  label = NULL,
  scale = TRUE,
  center = TRUE,
  xAxis = "PC1",
  yAxis = "PC2",
  shape = FALSE,
  ellipses = TRUE,
  title = "PCA",
  legendPosition = "bottom",
  labelSize = 2,
  ...
)

## S4 method for signature 'AnalysisData'
plotPCA(
  analysis,
  cls = "class",
  label = NULL,
  scale = TRUE,
  center = TRUE,
  xAxis = "PC1",
  yAxis = "PC2",
  shape = FALSE,
  ellipses = TRUE,
  title = "Principle Component Analysis (PCA)",
  legendPosition = "bottom",
  labelSize = 2
)

## S4 method for signature 'Analysis'
plotPCA(
  analysis,
  cls = "class",
  label = NULL,
  scale = TRUE,
  center = TRUE,
  xAxis = "PC1",
  yAxis = "PC2",
  shape = FALSE,
  ellipses = TRUE,
  title = "PCA",
  legendPosition = "bottom",
  labelSize = 2,
  type = c("pre-treated", "raw")
)

Arguments

analysis	object of class AnalysisData or Analysis
cls	name of class information column to use for sample labelling
label	name of class information column to use for sample labels. Set to NULL for no labels.
scale	scale the data
center	center the data
xAxis	principle component to plot on the x-axis
yAxis	principle component to plot on the y-axis
shape	TRUE/FALSE use shape aesthetic for plot points. Defaults to TRUE when the number of classes is greater than 12
ellipses	TRUE/FALSE, plot multivariate normal distribution 95\ confidence ellipses for each class
title	plot title
legendPosition	legend position to pass to legend.position argument of ggplot2::theme. Set to "none" to remove legend.
labelSize	label size. Ignored if label is NULL
...	arguments to pass to the appropriate method
type	raw or pre-treated data to plot

Examples

library(metaboData)

d <- analysisData(abr1$neg,abr1$fact) %>% 
 occupancyMaximum(cls = 'day')

## PCA plot
plotPCA(d,cls = 'day')

jasenfinch/metabolyseR documentation built on Sept. 18, 2023, 1:25 a.m.