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", ... )
| 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 |
| default_save_name | default save name for saving, don't change, change save_name in save_param |
| ... | additional parameters |
plotly
Description of parameters.