Plot cell abundances across groups in a Seurat object

Usage

AbundancePlot(
  object,
  group.by,
  split.by,
  replicate.by,
  draw_paths = FALSE,
  perform.stat.test = TRUE,
  test.choice = "t.test",
  ncols = 3,
  paired = FALSE,
  set_minimum_to_zero = FALSE,
  fill_colors = NULL,
  point_colors = NULL,
  p.adjust.method = "BH",
  filter.p.above = 1,
  step.increase = 0.15,
  title_size = 10,
  p_val_size = 2.5,
  plot_type = "box",
  bees = TRUE,
  x_lab = NULL,
  y_lab = NULL,
  point_size = 1,
  same_y_limit = FALSE,
  selected.groups = NULL,
  rotated_axis = FALSE,
  print_results = FALSE
)

Arguments

object: Seurat object
group.by: Which meta.data slot to use for grouping the cells
split.by: Which meta.data slot to use for splitting the groups
replicate.by: Which meta.data slot to use as split.by replicates
draw_paths: Whether or not to draw paths in the abundance plots between replicates if they exist
perform.stat.test: Whether or not to perform a statistical test between the splits
test.choice: Which choice of test to use (supports t.test of wilcox)
ncols: Number of columns to plot the groups as
paired: Whether the t.test should be paired if using t.test
set_minimum_to_zero: Whether to set minimum abundance on plots to 0 globally
point_colors: Vector of colors to color points as
p.adjust.method: Which method to use for p-value adjustment for mulitple testing
filter.p.above: Plot p-values only below this filter
step.increase: Tweaking the space between brackets for p-values vertically
title_size: Text size of each group plot's title
p_val_size: Text size for p-values
plot_type: Either box or violin plot
x_lab: The label on the x axis
y_lab: The label on the y axis
point_size: Size of the points plotted
same_y_limit: Whether to keep the upper y limit constant across all groups.
selected.groups: Optional. If not NULL, will only plot the groups specified in this argument.
rotated_axis: Whether to apply Seurat::RotatedAxis to the plots
print_results: Prints to screen the results of the abundance calculations ($freq) and abundance statistical testing ($pvals) in a list.
sina_shift: Whether to use ggforce::geom_sina to pretty-shift the points

Value

Returns a patchwork plot of separate ggplots per group.by variable

Details

Plots the abundances of specific groups in the Seurat object across a split.by variable, using replicate.by as replicates for each split.by condition