cellProximitySpatPlot2D#
Last Updated: Oct 02, 2023
Description#
Visualize 2D cell-cell interactions according to spatial coordinates in ggplot mode
Usage#
cellProximitySpatPlot2D(
gobject,
spat_unit = NULL,
feat_type = NULL,
spat_loc_name = NULL,
interaction_name = NULL,
cluster_column = NULL,
sdimx = "sdimx",
sdimy = "sdimy",
cell_color = NULL,
cell_color_code = NULL,
color_as_factor = T,
show_other_cells = F,
show_network = F,
show_other_network = F,
network_color = NULL,
spatial_network_name = "Delaunay_network",
show_grid = F,
grid_color = NULL,
spatial_grid_name = "spatial_grid",
coord_fix_ratio = 1,
show_legend = T,
point_size_select = 2,
point_select_border_col = "black",
point_select_border_stroke = 0.05,
point_size_other = 1,
point_alpha_other = 0.3,
point_other_border_col = "lightgrey",
point_other_border_stroke = 0.01,
show_plot = NA,
return_plot = NA,
save_plot = NA,
save_param = list(),
default_save_name = "cellProximitySpatPlot2D"
)
Arguments#
|
giotto object |
|
spatial unit |
|
feature type |
|
spatial locations to use |
|
cell-cell interaction name |
|
cluster column with cell clusters |
|
x-axis dimension name (default = ‘sdimx’) |
|
y-axis dimension name (default = ‘sdimy’) |
|
color for cells (see details) |
|
named vector with colors |
|
convert color column to factor |
|
decide if show cells not in network |
|
show spatial network of selected cells |
|
show spatial network of not selected cells |
|
color of spatial network |
|
name of spatial network to use |
|
show spatial grid |
|
color of spatial grid |
|
name of spatial grid to use |
|
fix ratio between x and y-axis |
|
show legend |
|
size of selected points |
|
border color of selected points |
|
stroke size of selected points |
|
size of other points |
|
opacity of other points |
|
border color of other points |
|
stroke size of other points |
|
show plots |
|
return ggplot object |
|
directly save the plot [boolean] |
|
list of saving parameters from
|
|
default save name for saving, don’t change, change save_name in save_param |
Details#
Description of parameters.
Value#
ggplot