plot_hexbin_meta: Plot of meta data of single cell data in bivariate hexagon...

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

Plot of meta data of single cell data in bivariate hexagon cells.

Description

Plot of meta data of single cell data in bivariate hexagon cells.

Usage

plot_hexbin_meta(
  sce,
  col,
  action,
  no = 1,
  colors = NULL,
  title = NULL,
  xlab = NULL,
  ylab = NULL,
  na.rm = FALSE
)

Arguments

sce	A SingleCellExperiment object.
col	A string referring to the name of one column in the meta data of sce by which to colour the hexagons.
action	A string specifying how meta data of observations in binned hexagon cells are to be summarized. Possible actions are majority, prop, prop_0, mode, mean and median (see details).
no	An integer specifying which level to plot of the column. Only in effect when action=prop.
colors	A vector of strings specifying which colors to use for plotting the different levels in the selected column of the meta data. Only in effect when the selected action="majority".
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.
na.rm	Logical indicating whether NA values should be removed.

Details

This function plots any column of the meta data in the hexagon cell representation calculated with make_hexbin. The chosen meta data column is summarized by one of six actions majority, prop, prop_0, mode, mean and median:

majority

Returns the value of the majority of observations in the bin. The associated meta data column needs to be a factor or character.

prop

Returns the proportion of each level or unique character in the bin. The associated meta data column needs to be a factor or character

prop_0

Returns the proportion of observations in the b factor or character 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, ]
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, 20, dimension_reduction = "PCA")
plot_hexbin_meta(tenx_pbmc3k, col = "total", action = "median")

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