Visualize 2D cell-cell interactions according to spatial coordinates in ggplot mode
cellProximitySpatPlot(gobject, ...)
giotto object
Arguments passed on to cellProximitySpatPlot2D
interaction_name
cell-cell interaction name
cluster_column
cluster column with cell clusters
sdimx
x-axis dimension name (default = 'sdimx')
sdimy
y-axis dimension name (default = 'sdimy')
cell_color
color for cells (see details)
cell_color_code
named vector with colors
color_as_factor
convert color column to factor
show_other_cells
decide if show cells not in network
show_network
show spatial network of selected cells
show_other_network
show spatial network of not selected cells
network_color
color of spatial network
spatial_network_name
name of spatial network to use
show_grid
show spatial grid
grid_color
color of spatial grid
spatial_grid_name
name of spatial grid to use
coord_fix_ratio
fix ratio between x and y-axis
show_legend
show legend
point_size_select
size of selected points
point_select_border_col
border color of selected points
point_select_border_stroke
stroke size of selected points
point_size_other
size of other points
point_alpha_other
opacity of other points
point_other_border_col
border color of other points
point_other_border_stroke
stroke size of other points
show_plot
show plots
return_plot
return ggplot object
save_plot
directly save the plot [boolean]
save_param
list of saving parameters from all_plots_save_function
default_save_name
default save name for saving, don't change, change save_name in save_param
ggplot
Description of parameters.
cellProximitySpatPlot2D
and cellProximitySpatPlot3D
for 3D