plotClustersSimilarity: plotClustersSimilarity

In ilyessr/conclus: ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion

plotClustersSimilarity

Description

This function plots the clusters similarity matrix as a heatmap.

Usage

plotClustersSimilarity(theObject, colorPalette="default",
statePalette="default", clusteringMethod="ward.D2", returnPlot=FALSE,
savePlot=FALSE, plotPDF=TRUE, width=7, height=5.5, onefile=FALSE,
fontsize=7.5, widthPNG=800, heightPNG=750, silentPlot=FALSE)

Arguments

theObject	A scRNAseq object with the cluster similarity matrix obtained with ?calculateClustersSimilarity.
colorPalette	A vector of colors for clusters. Default = "default", see details.
statePalette	A vector of colors for states or conditions. See details.
clusteringMethod	Clustering method passed to hclust() function. See ?hclust for a list of method. Default = "ward.D2"
returnPlot	Boolean indicating if the pHeatmap object should be returned by the function. Default = FALSE.
savePlot	If TRUE and plotPDF=TRUE, save the heatmap in pdf format. The heatmap is saved in the output directory defined in theObject (?getOutputDirectory) and in the sub-directory 'pictures'.
plotPDF	If TRUE, the heatmap is saved in pdf format and in png otherwise. Default = TRUE.
width	Width of the plot in the pdf file. See ?pdf for more details. Default = 7.
height	Height of the plot in the pdf file. See ?pdf for more details. Default = 5.5.
onefile	Logical: if TRUE allow multiple figures in one file. If FALSE, generate a file with name containing the page number for each page. Defaults to FALSE.
fontsize	pheatmap parameter. Base fontsize for the plot. Default=7.5.
widthPNG	Width of the png. See ?png for details. Default=800.
heightPNG	Height of the png. See ?png for details. Default=750.
silentPlot	If TRUE, does not plot the pheatmap. Default=FALSE. This is useful if one wants to only retrieve the object to insert the figure in a grid for instance.

Details

colorPalette/statePalette – A vector of colors for clusters/states or 'default' value. If 'default' is selected, the number of clusters is limited to 16. If an error message is thrown, re-run the function with your own color vector.

Value

A pheatmap object of the clusters similarity matrix.

Author(s)

Ilyess RACHEDI, based on code by Polina PAVLOVICH and Nicolas DESCOSTES.

See Also

calculateClustersSimilarity plotClusteredTSNE plotCellHeatmap plotGeneExpression plotCellSimilarity

Examples

## Object scr containing the results of previous steps
load(system.file("extdata/scrFull.Rdat", package="conclus"))

## Plot similarity matrix as a heatmap
plotClustersSimilarity(scr)

ilyessr/conclus documentation built on April 8, 2022, 1:43 p.m.