plotScanpyEmbedding

plotScanpyEmbedding

plotScanpyEmbedding(
  inSCE,
  reducedDimName,
  useAssay = NULL,
  color = NULL,
  legend = "right margin",
  title = ""
)

Arguments

inSCE

Input SingleCellExperiment object.

reducedDimName

Name of reducedDims object containing embeddings. Eg. scanpyUMAP.

useAssay

Specify name of assay to use. Default is NULL, which will use scaled assay by default.

color

Keys for annotations of observations/cells or variables/genes.

legend

Location of legend, either 'on data', 'right margin' or a valid keyword for the loc parameter of Legend.

title

Provide title for panels either as string or list of strings

Value

plot object

Examples

data(scExample, package = "singleCellTK")
if (FALSE) {
sce <- runScanpyNormalizeData(sce, useAssay = "counts")
sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
sce <- runScanpyPCA(sce, useAssay = "scanpyScaledData")
sce <- runScanpyFindClusters(sce, useReducedDim = "scanpyPCA")
sce <- runScanpyUMAP(sce, useReducedDim = "scanpyPCA")
plotScanpyEmbedding(sce, reducedDimName = "scanpyUMAP", color = 'Scanpy_louvain_1')
}