plotMDS: Multidimensional scaling (MDS) plot

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

Multidimensional scaling (MDS) plot

Description

Plot multidimensional scaling plot for a RandomForest class object.

Usage

plotMDS(
  x,
  cls = "class",
  label = NULL,
  shape = FALSE,
  ellipses = TRUE,
  title = "",
  legendPosition = "bottom",
  labelSize = 2
)

## S4 method for signature 'RandomForest'
plotMDS(
  x,
  cls = "class",
  label = NULL,
  shape = FALSE,
  ellipses = TRUE,
  title = "",
  legendPosition = "bottom",
  labelSize = 2
)

## S4 method for signature 'list'
plotMDS(
  x,
  label = NULL,
  shape = FALSE,
  ellipses = TRUE,
  title = "",
  legendPosition = "bottom",
  labelSize = 2
)

Arguments

x	S4 object of class RandomForest
cls	sample information column to use for sample labelling, Set to NULL for no labelling.
label	sample information column to use for sample labels. Set to NULL for no labels.
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

Examples

library(metaboData)

x <- analysisData(abr1$neg[,200:300],abr1$fact) %>%
       occupancyMaximum(cls = 'day') %>%
       transformTICnorm()
       
rf <- randomForest(x,cls = 'day')

plotMDS(rf,cls = 'day')

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