plotCellHeatmap: plotCellHeatmap

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

plotCellHeatmap

Description

This function plots heatmap with marker genes on rows and clustered cells on columns.

Usage

plotCellHeatmap(theObject, fileName = NA, meanCentered=TRUE,
                colorPalette="default", statePalette="default",
                clusteringMethod="ward.D2", orderClusters=FALSE,
                orderGenes=FALSE, returnPlot=FALSE, savePlot=FALSE, width=10,
                height=8.5, onefile=FALSE, clusterCols=FALSE,
                showColnames=FALSE, fontsize=7.5,  fontsizeRow=8,
                plotPDF=TRUE, widthPNG=800, heightPNG=750, silentPlot)

Arguments

theObject	A scRNAseq object with the cluster similarity matrix obtained with ?calculateClustersSimilarity method and the top markers obtained with ?retrieveTopClustersMarkers.
fileName	Name of the output file to which the heatmap is saved.
meanCentered	Boolean indicating if mean centering should be applied to the expression matrix. Default = TRUE.
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.
orderGenes	Boolean, should the heatmap be structured by gene. Default = FALSE.
returnPlot	If TRUE returns a pheatmap object. 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'.
width	Width of the plot in the pdf file. See ?pdf for more details. Default = 10.
height	Height of the plot in the pdf file. See ?pdf for more details. Default = 8.5.
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.
clusterCols	If TRUE, the columns representing the clusters are also taken into account in the hierarchical clustering. Default=FALSE.
showColnames	Shoud the names of the columns (clusters) be indicated on the heatmap. Default = FALSE.
fontsize	Base fontsize for the plot. Default = 7.5.
fontsizeRow	Fontsize for rownames. Default = 8.
plotPDF	If TRUE, the heatmap is saved in pdf format and in png otherwise. Default = TRUE.
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.

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 heatmap if returnPlot is TRUE.

Author(s)

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

See Also

calculateClustersSimilarity plotClusteredTSNE plotCellSimilarity plotGeneExpression plotClustersSimilarity

Examples

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

## Plot the heatmap with marker genes
plotCellHeatmap(scr)

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