plotBiomarker {singleCellTK} | R Documentation

## 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", 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")

[Package singleCellTK version 1.4.2 Index]