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 = TRUE,
show_other_cells = TRUE,
show_network = TRUE,
show_other_network = FALSE,
network_color = NULL,
spatial_network_name = "Delaunay_network",
show_grid = FALSE,
grid_color = NULL,
spatial_grid_name = "spatial_grid",
show_legend = TRUE,
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 = NULL,
return_plot = NULL,
save_plot = NULL,
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')
character. what to color cells by (e.g. metadata col or spatial enrichment col)
character. discrete colors to use. palette to use or named vector of colors
logical. convert color column to factor. discrete colors are used when this is TRUE. continuous colors when FALSE.
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
logical. 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
logical. show plot
logical. return ggplot object
logical. save the plot
list of saving parameters, see
showSaveParameters
default save name for saving, don't change, change save_name in save_param
additional parameters
plotly
Description of parameters.