plotExprsFreqVsMean: Plot expression frequency against mean counts

In ycl6/scRUtils: Single-Cell Sequencing Analysis Utilities

Plot expression frequency against mean counts

Description

This function uses plotRowData() from the scater package to produce a scatter plot of expression frequency against mean counts by using per-feature quality control metrics produced by scuttle.

Usage

plotExprsFreqVsMean(
  sce,
  point_size = 2,
  point_alpha = 0.8,
  anno_size = 6,
  text_size = 4,
  text_color = "black",
  trend_color = "firebrick",
  trend_size = 1,
  trend_se = TRUE,
  box.padding = 0.5,
  max.overlaps = Inf,
  seed = 12321,
  xlab = "log2 Mean expression",
  ylab = "Percentage of expressing cells",
  title = NULL,
  theme_size = 18,
  ...
)

Arguments

sce	A SingleCellExperiment object containing the required QC metrics for features ('mean' and 'detected') that were returned by addPerCellQC() or perFeatureQCMetrics() in its rowData slot.
point_size	A numeric scalar indicating the size of the points. Default is 2.
point_alpha	A numeric scalar (between 0 and 1) indicating the transparency. Default is 0.8.
anno_size	A numeric scalar indicating the size of annotation text. Default is 6.
text_size	A numeric scalar indicating the size of the label. This is passed to geom_text_repel(). Default is 4.
text_color	A string indicating the colour of the label. This is passed to geom_text_repel(). Default is "black".
trend_color	A string indicating the colour of the smoothed curve. Default is "firebrick",
trend_size	A numeric scalar indicating the size of the smoothed curve. Default is 1.
trend_se	Logical scalar indicating whether to display confidence interval around smooth. Default is TRUE.
box.padding	A scalar indicating the amount of padding around bounding box, as unit or number. This is passed to geom_text_repel(). Default is 0.5.
max.overlaps	Exclude text labels that overlap too many things. This is passed to geom_text_repel(). Default is Inf.
seed	Random seed passed to set.seed(). This is passed to geom_text_repel(). Default is 12321.
xlab	The title of the x-axis. Default is "log2 Mean expression".
ylab	The title of the y-axis. Default is "Percentage of expressing cells".
title	Plot title. Default is NULL.
theme_size	A numeric scalar indicating the base font size. Default is 18.
...	Other arguments passed on to geom_text_repel().

Details

The original function of the same name can be found in the legacy scater package and is now deprecated.

Value

A ggplot object

Author(s)

I-Hsuan Lin

See Also

scater::plotRowData(), scuttle::addPerFeatureQCMetrics(), scuttle::perFeatureQCMetrics(), ggrepel::geom_text_repel()

Examples

library(SingleCellExperiment)

# Load demo dataset
data(sce)

plotExprsFreqVsMean(sce, title = "Expression frequency vs. mean expression level")

ycl6/scRUtils documentation built on Feb. 18, 2025, 6:14 a.m.