plot_hexbin_gene: Plot of gene expression of single cells in bivariate hexagon...

In schex: Hexbin plots for single cell omics data

Description

Plot of gene expression of single cells in bivariate hexagon cells.

Usage

plot_hexbin_gene(
  sce,
  type,
  gene,
  action,
  title = NULL,
  xlab = NULL,
  ylab = NULL
)

## S4 method for signature 'SingleCellExperiment'
plot_hexbin_gene(
  sce,
  type,
  gene,
  action,
  title = NULL,
  xlab = NULL,
  ylab = NULL
)

## S4 method for signature 'Seurat'
plot_hexbin_gene(
  sce,
  type,
  gene,
  action,
  title = NULL,
  xlab = NULL,
  ylab = NULL
)

Arguments

sce	A SingleCellExperiment or 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.
gene	A string referring to the name of one gene.
action	A strings pecifying how gene expression of observations in binned hexagon cells are to be summarized. Possible actions are prop_0, mode, mean and median (see details).
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 expression of any gene in the hexagon cell representation calculated with make_hexbin. The chosen gene expression is summarized by one of four actions prop_0, mode, mean and median:

prop_0

Returns the proportion of observations in the bin greater than 0. The associated meta data column needs to be numeric.

mode

Returns the mode of the observations in the bin. The associated meta data column needs to be numeric.

mean

Returns the mean of the observations in the bin. The associated meta data column needs to be numeric.

median

Returns the median of the observations in the bin. The associated meta data column needs to be numeric.

Value

A ggplot2{ggplot} object.

Methods (by class)

• SingleCellExperiment: Plot of gene expression into hexagon cell for SingleCellExperiment object.

• Seurat: Plot of gene expression into hexagon cell for Seurat object.

Examples

# For Seurat object
library(Seurat)
data("pbmc_small")
pbmc_small <- make_hexbin(pbmc_small, 10, dimension_reduction = "PCA")
plot_hexbin_gene(pbmc_small, type = "counts", gene = "TALDO1", 
    action = "prop_0")

schex documentation built on Nov. 8, 2020, 5:56 p.m.