plotClusteredTSNE-scRNAseq: plotClusteredTSNE

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

plotClusteredTSNE

Description

Plot t-SNE generated with different PCs and perplexities. It can also use a coloring scheme by clusters or states. The latter is possible if a 'state' column, representing conditions, is provided in the columns meta-data.

Usage

plotClusteredTSNE(theObject, colorPalette="default",
            PCs=c(4, 6, 8, 10, 20, 40, 50), perplexities=c(30, 40),
            columnName="clusters", savePlot=FALSE, plotPDF=TRUE,
            returnPlot=FALSE, width=6, height=5, onefile=FALSE, widthPNG=800,
            heightPNG=750, silentPlot=FALSE, tSNENb=NA)

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.
PCs	A vector of first principal components. For example, to take ranges 1:5 and 1:10 write c(5, 10). Default = c(4, 6, 8, 10, 20, 40, 50). See ?generateTSNECoordinates for details.
perplexities	Numeric scalar defining the perplexity parameter, see ?Rtsne and ?generateTSNECoordinates for more details. Default = c(30, 40)
columnName	Name of the column to color the t-SNE with. Possible values are clusters, noColor, or state.
savePlot	If TRUE, the heatmap is saved in the directory defined in theObject (?getOutputDirectory) and in the sub-directory "pictures/tSNE_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 = FALSE.
width	Width of the plot in the pdf file. See ?pdf for more details. Default = 6.
height	Height of the plot in the pdf file. See ?pdf for more details. Default = 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.
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, the plots are not displayed on the current device. Default=FALSE.
tSNENb	Give the number of the tSNE to plot. If NA, all tSNE solutions are plotted (14 tSNE by default). Default=NA.

Details

colorPalette – 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 list of ggplot objects if returnPlot is TRUE.

Author(s)

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

See Also

calculateClustersSimilarity plotCellSimilarity 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
plotClusteredTSNE(scr, tSNENb=1)

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