plotDimRed: Plot results either on already run results of reduced...

In mmkhan19/singleCellTK: Interactive Analysis of Single Cell RNA-Seq Data

Plot results either on already run results of reduced dimensions data.

Description

Plot results either on already run results of reduced dimensions data.

Usage

plotDimRed(
  inSCE,
  colorBy = "No Color",
  shape = "No Shape",
  reducedDimName = NULL,
  useAssay = "logcounts",
  comp1 = NULL,
  comp2 = NULL,
  pcX = NULL,
  pcY = NULL
)

Arguments

inSCE	Input SCtkExperiment object with saved dimension reduction components or a variable with saved results. Required
colorBy	color by a condition(any column of the annotation data).
shape	add shapes to each condition.
reducedDimName	saved dimension reduction name in the SCtkExperiment object. Required.
useAssay	Indicate which assay to use. The default is "logcounts"
comp1	label for x-axis
comp2	label for y-axis
pcX	PCA component to be used for plotting(if applicable). Default is first PCA component for PCA data and NULL otherwise.
pcY	PCA component to be used for plotting(if applicable). Default is second PCA component for PCA data and NULL otherwise.

Value

a ggplot of the reduced dimensions.

Examples

plotDimRed(inSCE = mouseBrainSubsetSCE, colorBy = "No Color", shape = "No Shape",
           reducedDimName = "TSNE_counts", useAssay = "counts",
           comp1 = "tSNE1", comp2 = "tSNE2")

mmkhan19/singleCellTK documentation built on March 22, 2022, 7:43 a.m.