plotScanpyPCA: plotScanpyPCA

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

plotScanpyPCA

Description

plotScanpyPCA

Usage

plotScanpyPCA(
  inSCE,
  reducedDimName = "scanpyPCA",
  color = NULL,
  title = "",
  legend = "right margin"
)

Arguments

inSCE	Input SingleCellExperiment object.
reducedDimName	Name of new reducedDims object containing Scanpy PCA.
color	Keys for annotations of observations/cells or variables/genes.
title	Provide title for panels either as string or list of strings
legend	Location of legend, either 'on data', 'right margin' or a valid keyword for the loc parameter of Legend.

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")
plotScanpyPCA(sce)

## End(Not run)

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