plot_hexbin_bivariate: Plot of feature expression and uncertainty of single cells in...
In schex: Hexbin plots for single cell omics data

Description Usage Arguments Details Value Examples

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

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

`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.

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".

A ggplot2{ggplot} object.

# 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)