plotCellSimilarity-scRNAseq: plotCellSimilarity

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

plotCellSimilarity

Description

This function plots the similarity matrix as a heatmap.

Usage

plotCellSimilarity(theObject, colorPalette="default",
            statePalette="default", clusteringMethod="ward.D2",
            orderClusters=FALSE, savePlot=FALSE, plotPDF=TRUE,
            returnPlot=FALSE, width=7, height=6, onefile=FALSE,
            showRowNames=FALSE, showColnames=FALSE, fontsize=7.5,
            fontsizeRow=0.03, widthPNG=800, heightPNG=750, silentPlot=FALSE)

Arguments

theObject	An Object of class scRNASeq for which the count matrix was normalized (see ?normaliseCountMatrix), tSNE were calculated (see ?generateTSNECoordinates), dbScan was run (see ?runDBSCAN), cells were clustered (see ?clusterCellsInternal), as clusters themselves (see ?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"
orderClusters	If TRUE, clusters in the similarity matrix of cells will be ordered by name. Default = FALSE.
savePlot	If TRUE, the heatmap is saved in the directory defined in theObject (?getOutputDirectory) and in the sub-directory "pictures".
plotPDF	If TRUE export heatmap in pdf format, if FALSE export it in png format. Default=TRUE.
returnPlot	Boolean indicating if the pHeatmap object should be returned by the function. 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 = 6.
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.
showRowNames	pheatmap parameter. Boolean specifying if row names are displayed. Default=FALSE.
showColnames	pheatmap parameter. Boolean specifying if column names are displayed. Default=FALSE.
fontsize	pheatmap parameter. Base fontsize for the plot. Default=7.5.
fontsizeRow	pheatmap parameter. Fontsize for rownames. Default=0.03.
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 heatmap. Default=FALSE.

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 similarity heatmap if returnPlot is TRUE.

Author(s)

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

See Also

calculateClustersSimilarity plotClusteredTSNE plotCellHeatmap plotGeneExpression plotClustersSimilarity

Examples

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

## Plot the heatmap of the similarity matrix
plotCellSimilarity(scr)

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