parafac4microbiome (version 1.1.2)

plotModelStability: Plot a summary of the loadings of many initialized parafac models.

Description

Plot a summary of the loadings of many initialized parafac models.

Usage

plotModelStability(
  models,
  dataset,
  colourCols = NULL,
  legendTitles = NULL,
  xLabels = NULL,
  legendColNums = NULL,
  arrangeModes = NULL,
  continuousModes = NULL,
  overallTitle = ""
)

Value

Plot of loadings with error bars

Arguments

models

Models list output from parafac() using output="all".

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.

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

processedFujita = processDataCube(Fujita2023, sparsityThreshold=0.99, centerMode=1, scaleMode=2)
models = parafac(processedFujita$data, 2, nstart=10, output="all")
plotModelStability(models, processedFujita)