plotBiomarker: Given a set of genes, return a ggplot of expression values.

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

Given a set of genes, return a ggplot of expression values.

Description

Given a set of genes, return a ggplot of expression values.

Usage

plotBiomarker(
  inSCE,
  gene,
  binary = "Binary",
  shape = "No Shape",
  useAssay = "counts",
  reducedDimName = "PCA",
  x = NULL,
  y = NULL,
  comp1 = NULL,
  comp2 = NULL
)

Arguments

inSCE	Input SCtkExperiment object. Required
gene	genelist to run the method on.
binary	binary/continuous color for the expression.
shape	shape parameter for the ggplot.
useAssay	Indicate which assay to use. The default is "logcounts".
reducedDimName	results name of dimension reduction coordinates obtained from this method. This is stored in the SingleCellExperiment object in the reducedDims slot. Required.
x	PCA component to be used for plotting(if applicable). Default is first PCA component for PCA data and NULL otherwise.
y	PCA component to be used for plotting(if applicable). Default is second PCA component for PCA data and NULL otherwise.
comp1	label for x-axis
comp2	label for y-axis

Value

A Biomarker plot

Examples

data("mouseBrainSubsetSCE")
plotBiomarker(mouseBrainSubsetSCE, gene="C1qa", shape="level1class", reducedDimName="TSNE_counts")

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