Visualize Cell-Cell Interactions (3D)

cellProximitySpatPlot3D()

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",
    ...
)

Arguments

gobject	giotto object
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’)
sdimz	z-axis dimension name (default = ‘sdimz’)
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
show_legend	show legend
point_size_select	size of selected points
point_size_other	size of other points
point_alpha_other	opacity of other points
axis_scale	scale of axis
custom_ratio	custom ratio of axes
x_ticks	ticks on x-axis
y_ticks	ticks on y-axis
z_ticks	ticks on z-axis
show_plot	show plots
return_plot	return plotly 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
…	additional parameters

Value

An plotly.

Details

Description of parameters.