plot_hexbin_bivariate {schex} | R Documentation

## Plot of feature expression and uncertainty of single cells in bivariate hexagon cells.

### Description

Plot of feature expression and uncertainty of single cells in bivariate hexagon cells.

### Usage

    plot_hexbin_bivariate(
      sce,
      mod = "RNA",
      type,
      feature,
      fan = FALSE,
      title = NULL,
      xlab = NULL,
      ylab = NULL
    )

### Arguments

`sce` | A `SingleCellExperiment` or `Seurat-class` object.
`mod` | A string referring to the name of the modality used for plotting. For RNA modality use "RNA". For other modalities use name of alternative object for the `SingleCellExperiment` or the name of the assay for the `Seurat-class` object.
`type` | A string referring to the type of assay in the `SingleCellExperiment` object or the data transformation in the `Seurat-class` object.
`feature` | A string referring to the name of one feature.
`fan` | Logical indicating whether to plot uncertainty surpressing palette.
`title` | A string containing the title of the plot.
`xlab` | A string containing the title of the x axis.
`ylab` | A string containing the title of the y axis.

### Details

This function plots the mean expression and a measure of uncertainty of any feature in the hexagon cell representation calculated with `make_hexbin` using a bivariate scale. When `fan=FALSE`, the standard deviation and the mean expression are plotted. When `fan=TRUE`, the mean expression and coefficient of variation are calculated. The coefficient of variation is converted to a percentage of uncertainty. When using `fan=TRUE` the raw count data should be used. In order to enable the calculation of the coefficient of variation a pseduo-count of 1 is added to every count.

To access the data that has been integrated in the `Seurat-class` object specifiy `mod="integrated"`.

### Value

A `ggplot2{ggplot}` object.

### Examples

    # For Seurat object
    library(Seurat)
    data("pbmc_small")
    pbmc_small <- make_hexbin(pbmc_small, 10, dimension_reduction = "PCA")
    plot_hexbin_bivariate(pbmc_small, type="counts", feature="CD3D")
    plot_hexbin_bivariate(pbmc_small, type="counts", feature="CD3D", fan=TRUE)

[Package schex version 1.8.0 Index]