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

plotBiomarker(inSCE, gene, binary = "Binary", visual = "PCA",
  shape = "No Shape", x = "PC1", y = "PC2", useAssay = "counts",
  reducedDimName = "PCA")

Arguments

inSCE

Input SCtkExperiment object. Required

gene

genelist to run the method on.

binary

binary/continuous color for the expression.

visual

Type of visualization (PCA, tSNE or UMAP). Default: "PCA"

shape

shape parameter for the ggplot.

x

x coordinate for PCA

y

y coordinate for PCA

useAssay

Indicate which assay to use. The default is "logcounts".

reducedDimName

a name to store the results of the dimension reduction coordinates obtained from this method. This is stored in the SingleCellExperiment object in the reducedDims slot. Required.

Value

A Biomarker plot

Examples

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