cellProximitySpatPlot#

Last Updated: Jan 29, 2024

Description#

Visualize 2D cell-cell interactions according to spatial coordinates in ggplot mode

Usage#

cellProximitySpatPlot(gobject, ...)

Arguments#

gobject

giotto object

...

Arguments passed on to cellProximitySpatPlot2D

feat_type

feature type

spat_unit

spatial unit

spat_loc_name

spatial locations to use

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

Details#

Description of parameters.

Value#

ggplot

See Also#

cellProximitySpatPlot2D and cellProximitySpatPlot3D for 3D