cellProximitySpatPlot#

Last Updated: Mar 11, 2023

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