Visualize 3D cell-cell interactions according to spatial coordinates in plotly mode
cellProximitySpatPlot3D(
gobject,
interaction_name = NULL,
cluster_column = NULL,
sdimx = "sdimx",
sdimy = "sdimy",
sdimz = "sdimz",
cell_color = NULL,
cell_color_code = NULL,
color_as_factor = T,
show_other_cells = T,
show_network = T,
show_other_network = F,
network_color = NULL,
spatial_network_name = "Delaunay_network",
show_grid = F,
grid_color = NULL,
spatial_grid_name = "spatial_grid",
show_legend = T,
point_size_select = 4,
point_size_other = 2,
point_alpha_other = 0.5,
axis_scale = c("cube", "real", "custom"),
custom_ratio = NULL,
x_ticks = NULL,
y_ticks = NULL,
z_ticks = NULL,
show_plot = NA,
return_plot = NA,
save_plot = NA,
save_param = list(),
default_save_name = "cellProximitySpatPlot3D",
...
)giotto object
cell-cell interaction name
cluster column with cell clusters
x-axis dimension name (default = 'sdimx')
y-axis dimension name (default = 'sdimy')
z-axis dimension name (default = 'sdimz')
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
show legend
size of selected points
size of other points
opacity of other points
scale of axis
custom ratio of axes
ticks on x-axis
ticks on y-axis
ticks on z-axis
show plots
return plotly object
directly save the plot [boolean]
list of saving parameters from all_plots_save_function
default save name for saving, don't change, change save_name in save_param
additional parameters
plotly
Description of parameters.