plotScanpyEmbedding: plotScanpyEmbedding

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

plotScanpyEmbedding

Description

plotScanpyEmbedding

Usage

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")
## Not run: 
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')

## End(Not run)

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.