R: Plot of external feature expression of single cells in...

plot_hexbin_feature {schex}

R Documentation

Plot of external feature expression of single cells in bivariate hexagon cells.

Description

Plot of external feature expression of single cells in bivariate hexagon cells.

Usage

plot_hexbin_feature(
  sce,
  mod,
  type,
  feature,
  action,
  title = NULL,
  xlab = NULL,
  ylab = NULL
)

## S4 method for signature 'SingleCellExperiment'
plot_hexbin_feature(
  sce,
  mod,
  type,
  feature,
  action,
  title = NULL,
  xlab = NULL,
  ylab = NULL
)

## S4 method for signature 'Seurat'
plot_hexbin_feature(
  sce,
  mod,
  type,
  feature,
  action,
  title = NULL,
  xlab = NULL,
  ylab = NULL
)

Arguments

`sce`	A `SingleCellExperiment` or `Seurat-class` object.
`mod`	A string referring to the name of the alternative object in a `SingleCellExperiment` or the assay in a `Seurat-class` object that stores the protein information.
`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 external feature.
`action`	A strings pecifying how meta data 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 feature 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")
protein <- matrix(rnorm(10* ncol(pbmc_small)), ncol=ncol(pbmc_small))
rownames(protein) <- paste0("A", seq(1,10,1))
colnames(protein) <- colnames(pbmc_small)
pbmc_small[["ADT"]] <- CreateAssayObject(counts = protein)
pbmc_small <- make_hexbin(pbmc_small, 10, dimension_reduction = "PCA")
plot_hexbin_feature(pbmc_small, type="counts", mod="ADT",
    feature="A1", action="prop_0")

[Package schex version 1.0.55 Index]