Plot dimensionality reduction from computed metrics including PCA, ICA, tSNE and UMAP

Source: R/plotDimRed.R

Plot dimensionality reduction from computed metrics including PCA, ICA, tSNE and UMAP

plotDimRed(
  inSCE,
  useReduction,
  showLegend = FALSE,
  xDim = 1,
  yDim = 2,
  xAxisLabel = NULL,
  yAxisLabel = NULL
)

Arguments

inSCE

Input SCE object

useReduction

Reduction to plot

showLegend

If legends should be plotted or not

xDim

Numeric value indicating the dimension to use for X-axis. Default is 1 (refers to PC1).

yDim

Numeric value indicating the dimension to use for Y-axis. Default is 2 (refers to PC2).

xAxisLabel

Specify the label for x-axis. Default is NULL which will specify the label as 'x'.

yAxisLabel

Specify the label for y-axis. Default is NULL which will specify the label as 'y'.

Value

plot object

Examples

data("mouseBrainSubsetSCE", package = "singleCellTK")
plotDimRed(mouseBrainSubsetSCE, "PCA_logcounts")