R/plotTSNE.R
plotTSNE.Rd
Plot t-SNE plot on dimensionality reduction data run from t-SNE method.
plotTSNE( inSCE, colorBy = "No Color", shape = "No Shape", reducedDimName = "TSNE", runTSNE = FALSE, useAssay = "logcounts" )
inSCE | Input SingleCellExperiment object. |
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colorBy | color by condition. |
shape | add shape to each distinct label. |
reducedDimName | a name to store the results of the dimension reduction coordinates obtained from this method. This is stored in the SingleCellExperiment object in the reducedDims slot. Required. |
runTSNE | Run t-SNE if the reducedDimName does not exist. the Default is FALSE. |
useAssay | Indicate which assay to use. The default is "logcounts". |
A t-SNE plot
data("mouseBrainSubsetSCE") plotTSNE(mouseBrainSubsetSCE, colorBy = "level1class", reducedDimName = "TSNE_counts")