Plot_Median_Genes {scCustomize}

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 = 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

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")