Plot Number of Cells/Nuclei per Sample — Plot_Cells_per

Plot of total cell or nuclei number per sample grouped by another meta data variable.

Plot_Cells_per_Sample(
  seurat_object,
  sample_col = "orig.ident",
  group.by = NULL,
  colors_use = NULL,
  dot_size = 1,
  plot_title = "Cells/Nuclei per Sample",
  y_axis_label = "Number of Cells",
  x_axis_label = NULL,
  legend_title = NULL,
  x_lab_rotate = TRUE,
  reorder = FALSE,
  reorder_decreasing = FALSE,
  plot_median = 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.
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.
reorder: logical, if plotting by sample should x-axis be reordered according to number of cells, default is FALSE.
reorder_decreasing: logical, if reorder = TRUE should points be ordered from fewest to greatest number of cells (FALSE) or reverse (TRUE), default is FALSE.
plot_median: logical, if plotting by sample should line be added showing median, default is TRUE.
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

if (FALSE) {
# Plot cells per sample grouped by "Diagnosis"
Plot_Cells_per_Sample(seurat_object = obj, sample_col = "orig.ident", group.by = "Diagnosis")

# Plot cells per sample individually
Plot_Cells_per_Sample(seurat_object = obj, sample_col = "orig.ident", group.by = "orig.ident")

#' # Plot cells per sample individually and reorder x-axis by cell number
Plot_Cells_per_Sample(seurat_object = obj, sample_col = "orig.ident", group.by = "orig.ident",
order = TRUE)

}