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

In SaskiaFreytag/schex: Hexbin plots for single cell omics data

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

Description

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

Usage

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

Arguments

sce	A SingleCellExperiment 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 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

# For SingleCellExperiment
library(TENxPBMCData)
library(scater)
tenx_pbmc3k <- TENxPBMCData(dataset = "pbmc3k")
rm_ind <- calculateAverage(tenx_pbmc3k) < 0.1
tenx_pbmc3k <- tenx_pbmc3k[!rm_ind, ]
colData(tenx_pbmc3k) <- cbind(colData(tenx_pbmc3k), perCellQCMetrics(tenx_pbmc3k))
tenx_pbmc3k <- logNormCounts(tenx_pbmc3k)
tenx_pbmc3k <- runPCA(tenx_pbmc3k)
tenx_pbmc3k <- make_hexbin(tenx_pbmc3k, 10, dimension_reduction = "PCA")
plot_hexbin_interact(tenx_pbmc3k,
    type = c("counts", "counts"), mod = c("RNA", "RNA"),
    feature = c("ENSG00000146109", "ENSG00000102265"), interact = "fc"
)

SaskiaFreytag/schex documentation built on Feb. 4, 2024, 7:49 p.m.