plot_cells_per_sample_and_perturbation: Make a boxplot of the number of cells per sample, with each...

In cole-trapnell-lab/monocle3: Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

Make a boxplot of the number of cells per sample, with each perturbation as a separate box. Optionally facet by a second value.

Description

Make a boxplot of the number of cells per sample, with each perturbation as a separate box. Optionally facet by a second value.

Usage

plot_cells_per_sample_and_perturbation(
  cds,
  perturbation_col = "perturbation",
  count_per_sample_col = "count_per_embryo",
  zscore = FALSE,
  cutoff = NULL,
  facet_by = NULL,
  color_palette = NULL,
  yticks = NULL
)

Arguments

cds	A cell_data_set for plotting.
perturbation_col	How to group the cells for the plot. Must be a column of the colData.
count_per_sample_col	Which column of the colData to put in the boxplots.
zscore	logical value indicating whether to z-score counts before plotting. If TRUE, then the values in count_per_sample_col are grouped by the perturbation_col and z-scored.
cutoff	The minimum number of cells per sample, drawn as a horizontal line. If zscore == TRUE then this corresponds to the absolute value of the z-score cutoff, and two horizontal lines are drawn.
facet_by	Facet the plot by this column of the colData. Each unique value is its own facet.
color_palette	List of colors to color perturbation groups. Default is NULL. When NULL, use a default set.
yticks	List of numeric values to put on the y-axis ticks.

Value

A ggplot2 object.

cole-trapnell-lab/monocle3 documentation built on June 11, 2025, 11:22 p.m.