plot_hexbin_interact: Plot of interaction of expression of single cells in...

Description Usage Arguments Details Value Examples

View source: R/plot_hexbin_interact.R

Description

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

Usage

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plot_hexbin_interact(
  sce,
  mod,
  type,
  feature,
  interact,
  title = NULL,
  xlab = NULL,
  ylab = NULL
)

Arguments

sce

A SingleCellExperiment or Seurat-class object.

mod

A vector of strings referring to the names of the modularities. For SingleCellExperiment use "RNA" to access the RNA expression data stored as the main experiment type.

type

A vector of strings referring to the types of assays in the SingleCellExperiment or the types of transformation in Seurat-class object.

feature

A vector of strings referring to the names of one features in the same order as the vector of modularities.

interact

A string specifying how interaction between features is calculated. Possible interaction measures are corr_spearman and mi (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 interaction between any features in the hexagon cell representation calculated with make_hexbin. The interaction between the chosen features is calculated by one of two measurers corr_spearman, ratio and mi:

mi

Returns the mutual information coefficient.

corr_spearman

Returns the Spearman correlation.

fc

Return the log fold change between the features.

Note that fc should be applied to log normalized values.

Value

A ggplot2{ggplot} object.

Examples

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# 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)
plot_hexbin_interact(pbmc_small, type=c("counts", "counts"),
    mod=c("RNA", "ADT"), feature=c("CD7", "A1"), interact="mi")

SaskiaFreytag/schex documentation built on June 6, 2021, 10:13 p.m.