Plot_Median_Genes: Plot Median Genes per Cell per Sample

In scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Plot Median Genes per Cell per Sample

Description

Plot of median genes per cell per sample grouped by desired meta data variable.

Usage

Plot_Median_Genes(
  seurat_object,
  sample_col = "orig.ident",
  group_by = deprecated(),
  group.by = NULL,
  colors_use = NULL,
  dot_size = 1,
  plot_title = "Median Genes/Cell per Sample",
  y_axis_label = "Median Genes",
  x_axis_label = NULL,
  legend_title = NULL,
  x_lab_rotate = TRUE,
  color_seed = 123
)

Arguments

seurat_object	Seurat object name.
sample_col	Specify which column in meta.data specifies sample ID (i.e. orig.ident).
group_by	soft-deprecated. See group.by.
group.by	Column in meta.data slot to group results by (i.e. "Treatment").
colors_use	List of colors or color palette to use. Only applicable if group.by is not NULL.
dot_size	size of the dots plotted if group.by is not NULL. Default is 1.
plot_title	Plot title.
y_axis_label	Label for y axis.
x_axis_label	Label for x axis.
legend_title	Label for plot legend.
x_lab_rotate	logical. Whether to rotate the axes labels on the x-axis. Default is FALSE.
color_seed	random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Value

A ggplot object

Examples

library(Seurat)
# Create example groups
pbmc_small$sample_id <- sample(c("sample1", "sample2"), size = ncol(pbmc_small), replace = TRUE)

# Plot
Plot_Median_Genes(seurat_object = pbmc_small, sample_col = "orig.ident",  group.by = "sample_id")

scCustomize documentation built on Aug. 26, 2025, 9:08 a.m.