Plot avereage feature expression per sample across groups in a Seurat object
ModulePlot.RdPlot avereage feature expression per sample across groups in a Seurat object
Usage
ModulePlot(
seurat_object,
assay = "AUC",
features = rownames(seurat_object[[assay]]),
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,
spacing_above = 1.3,
plot_type = "box",
sina_shift = TRUE,
x_lab = NULL,
y_lab = NULL,
same_y_limit = FALSE
)Arguments
- assay
Location of features (typically a gene module assay, not RNA...)
- features
Which features to use for grouping 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
- sina_shift
Whether to use ggforce::geom_sina to pretty-shift the points
- x_lab
The label on the x axis
- y_lab
The label on the y axis
- same_y_limit
Whether to keep the upper y limit constant across all groups.
- object
Seurat object
- point_size
Size of the points plotted