Visualize cell-cell communication using spatial plots with vector fields, arrows, or stream plots.
Usage
plot_cell_communication(
seurat_obj,
database_name,
lr_pair = NULL,
pathway_name = NULL,
spatial_coords = NULL,
plot_method = c("grid", "cell", "stream"),
color_by = "signal",
signal_type = c("sender", "receiver"),
arrow_scale = 1,
grid_resolution = 30L,
point_size = 1,
point_alpha = 0.8,
arrow_color = "black",
arrow_alpha = 0.6,
color_palette = NULL,
title = NULL,
legend_title = NULL,
theme_style = c("minimal", "void", "classic")
)Arguments
- seurat_obj
Seurat object with COMMOTR results.
- database_name
Database name.
- lr_pair
LR pair name (if NULL, uses pathway_name).
- pathway_name
Pathway name (if lr_pair is NULL).
- spatial_coords
Spatial coordinates or reduction name.
- plot_method
Method: "cell" (arrows at cells), "grid" (gridded arrows), "stream" (streamlines).
- color_by
Color points by: "signal", "sender", "receiver", or metadata column name.
- signal_type
For vector field: "sender" or "receiver".
- arrow_scale
Scale factor for arrows (default: 1).
- grid_resolution
Resolution for grid method (default: 30).
- point_size
Size of cell points (default: 1).
- point_alpha
Transparency of points (default: 0.8).
- arrow_color
Color for arrows (default: "black").
- arrow_alpha
Transparency of arrows (default: 0.6).
- color_palette
Color palette for continuous coloring.
- title
Plot title (default: auto).
- legend_title
Legend title.
- theme_style
Theme: "minimal" (default), "void", "classic".