scCustomize (version 3.0.0)

Plot_Median_Other: Plot Median other variable per Cell per Sample

Description

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

Usage

Plot_Median_Other(
  seurat_object,
  median_var,
  sample_col = "orig.ident",
  group_by = NULL,
  colors_use = NULL,
  dot_size = 1,
  plot_title = NULL,
  y_axis_label = NULL,
  x_axis_label = NULL,
  legend_title = NULL,
  x_lab_rotate = TRUE,
  color_seed = 123
)

Value

A ggplot object

Arguments

seurat_object

Seurat object name.

median_var

Variable in meta.data slot to calculate and plot median values for.

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.

Examples

if (FALSE) {
library(Seurat)
cd_features <- list(c('CD79B', 'CD79A', 'CD19', 'CD180', 'CD200', 'CD3D', 'CD2','CD3E',
'CD7','CD8A', 'CD14', 'CD1C', 'CD68', 'CD9', 'CD247'))

pbmc_small <- AddModuleScore(object = pbmc_small, features = cd_features, ctrl = 5,
name = 'CD_Features')

Plot_Median_Other(seurat_object = pbmc_small, median_var = "CD_Features1",
sample_col = "orig.ident", group_by = "Treatment")
}