Multidimensional scaling (MDS) plot — plotMDS • metabolyseR

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

# S4 method for 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')