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

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

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")