plot_hexbin_feature_plus: Plot of gene expression and meta data of single cell data in...

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

Plot of gene expression and meta data of single cell data in bivariate hexagon cells.

Description

Plot of gene expression and meta data of single cell data in bivariate hexagon cells.

Usage

plot_hexbin_feature_plus(
  sce,
  col,
  mod = "RNA",
  type,
  feature,
  action,
  colors = NULL,
  title = NULL,
  xlab = NULL,
  ylab = NULL,
  expand_hull = 3,
  ...
)

Arguments

sce	A SingleCellExperiment.
col	A string referring to the name of one column in the meta data of sce by which to colour the hexagons.
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 object.
type	A string referring to the type of assay in the SingleCellExperiment object.
feature	A string referring to the name of one feature.
action	A string specifying how gene expression of observations in binned hexagon cells are to be summarized. Possible actions are prop_0, mode, mean and median (see details).
colors	A vector of strings specifying which colors to use for plotting the different levels in the selected column of the meta data.
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.
expand_hull	A numeric value determining the expansion of the line marking different clusters.
...	Additional arguments passed on to ggforce{geom_mark_hull}.

Details

This function plots any gene expresssion in the hexagon cell representation calculated with make_hexbin as well as at the same time representing outlines of clusters. 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.

Examples

# For SingleCellExperiment object
library(TENxPBMCData)
library(scater)
tenx_pbmc3k <- TENxPBMCData(dataset = "pbmc3k")
rm_ind <- calculateAverage(tenx_pbmc3k) < 0.1
tenx_pbmc3k <- tenx_pbmc3k[!rm_ind, ]
tenx_pbmc3k <- logNormCounts(tenx_pbmc3k)
tenx_pbmc3k <- runPCA(tenx_pbmc3k)
tenx_pbmc3k <- make_hexbin(tenx_pbmc3k, 10, dimension_reduction = "PCA")
tenx_pbmc3k$random <- factor(sample(1:3, ncol(tenx_pbmc3k), replace = TRUE))
plot_hexbin_feature_plus(tenx_pbmc3k,
    col = "random", type = "counts",
    feature = "ENSG00000135250", action = "mean"
)

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