plotClusteredTSNE,scRNAseq-method {conclus} | R Documentation

## 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)

[Package conclus version 1.2.4 Index]