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",
      shape = "No Shape",
      useAssay = "counts",
      reducedDimName = "PCA",
      x = NULL,
      y = NULL,
      comp1 = NULL,
      comp2 = NULL
    )

### Arguments

`inSCE` | Input SingleCellExperiment object.
`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")

[Package singleCellTK version 2.2.0 Index]