parafac4microbiome (version 1.1.2)

plotPARAFACmodel: Plot a PARAFAC model

Description

Plot a PARAFAC model

Usage

plotPARAFACmodel(
  model,
  dataset,
  numComponents,
  colourCols = NULL,
  legendTitles = NULL,
  xLabels = NULL,
  legendColNums = NULL,
  arrangeModes = NULL,
  continuousModes = NULL,
  overallTitle = ""
)

Value

Plot object

Arguments

model

Model output from parafac().

dataset

A longitudinal microbiome dataset, ideally processed with processDataCube(), formatted as follows:

data

Array object of the data cube

mode1

Dataframe with all the subject metadata, ordered the same as the rows in the data cube.

mode2

Taxonomic classification of the microbiota, ordered the same as the columns in the data cube.

mode3

Dataframe with the time metadata, ordered the same as the third dimension in the array.

numComponents

Number of PARAFAC components in the model.

colourCols

Vector of strings stating which column names should be factorized for colours per mode.

legendTitles

Vector of strings stating the legend title per mode.

xLabels

Vector of strings stating the x-axis labels per mode.

legendColNums

Vector of integers stating the desired number of columns for the legends per mode.

arrangeModes

Vector of boolean values per mode, stating if the loadings should be arranged according to colourCols (TRUE) or not (FALSE).

continuousModes

Vector of boolean values per mode, stating if the loadings should be plotted as a line plot (TRUE) or a bar plot (FALSE).

overallTitle

Overall title of the plot.

Examples

library(multiway)
library(dplyr)
library(ggplot2)
set.seed(0)

# Process the data
processedFujita = processDataCube(Fujita2023, sparsityThreshold=0.9, centerMode=1, scaleMode=2)

# Make PARAFAC model
model = parafac(processedFujita$data, nfac=2, nstart=10, verbose=FALSE)

# Make plot
plotPARAFACmodel(model, processedFujita,
  numComponents = 2,
  colourCols = c("", "Genus", ""),
  legendTitles = c("", "Genus", ""),
  xLabels = c("Replicate", "Feature index", "Time point"),
  legendColNums = c(0,5,0),
  arrangeModes = c(FALSE, TRUE, FALSE),
  continuousModes = c(FALSE,FALSE,TRUE),
  overallTitle = "Fujita PARAFAC model")