Visualize cells according to spatial AND dimension reduction coordinates in plotly mode
spatDimPlot3D( gobject, plot_alignment = c("horizontal", "vertical"), dim_reduction_to_use = "umap", dim_reduction_name = "umap", dim1_to_use = 1, dim2_to_use = 2, dim3_to_use = 3, sdimx = "sdimx", sdimy = "sdimy", sdimz = "sdimz", spat_enr_names = NULL, show_NN_network = FALSE, nn_network_to_use = "sNN", network_name = "sNN.pca", nn_network_color = "lightgray", nn_network_alpha = 0.5, show_cluster_center = F, show_center_label = T, center_point_size = 4, label_size = 16, select_cell_groups = NULL, select_cells = NULL, show_other_cells = T, other_cell_color = "lightgrey", other_point_size = 1.5, cell_color = NULL, color_as_factor = T, cell_color_code = NULL, dim_point_size = 3, show_spatial_network = F, spatial_network_name = "Delaunay_network", spatial_network_color = "lightgray", spatial_network_alpha = 0.5, show_spatial_grid = F, spatial_grid_name = "spatial_grid", spatial_grid_color = NULL, spatial_grid_alpha = 0.5, spatial_point_size = 3, axis_scale = c("cube", "real", "custom"), custom_ratio = NULL, x_ticks = NULL, y_ticks = NULL, z_ticks = NULL, legend_text_size = 12, show_plot = NA, return_plot = NA, save_plot = NA, save_param = list(), default_save_name = "spatDimPlot3D" )
| gobject | giotto object |
|---|---|
| plot_alignment | direction to align plot |
| dim_reduction_to_use | dimension reduction to use |
| dim_reduction_name | dimension reduction name |
| dim1_to_use | dimension to use on x-axis |
| dim2_to_use | dimension to use on y-axis |
| dim3_to_use | dimension to use on z-axis |
| sdimx | = spatial dimension to use on x-axis |
| sdimy | = spatial dimension to use on y-axis |
| sdimz | = spatial dimension to use on z-axis |
| spat_enr_names | names of spatial enrichment results to include |
| show_NN_network | show underlying NN network |
| nn_network_to_use | type of NN network to use (kNN vs sNN) |
| network_name | name of NN network to use, if show_NN_network = TRUE |
| nn_network_color | color of nn network |
| nn_network_alpha | column to use for alpha of the edges |
| show_cluster_center | show the center of each cluster |
| show_center_label | provide a label for each cluster |
| center_point_size | size of the center point |
| label_size | size of the center label |
| select_cell_groups | select subset of cells/clusters based on cell_color parameter |
| select_cells | select subset of cells based on cell IDs |
| show_other_cells | display not selected cells |
| other_cell_color | color of not selected cells |
| other_point_size | size of not selected cells |
| cell_color | color for cells (see details) |
| color_as_factor | convert color column to factor |
| cell_color_code | named vector with colors |
| dim_point_size | size of points in dim. reduction space |
| show_spatial_network | show spatial network |
| spatial_network_name | name of spatial network to use |
| spatial_network_color | color of spatial network |
| spatial_network_alpha | alpha of spatial network |
| show_spatial_grid | show spatial grid |
| spatial_grid_name | name of spatial grid to use |
| spatial_grid_color | color of spatial grid |
| spatial_grid_alpha | alpha of spatial grid |
| spatial_point_size | size of spatial points |
| axis_scale | the way to scale the axis |
| custom_ratio | customize the scale of the plot |
| x_ticks | set the number of ticks on the x-axis |
| y_ticks | set the number of ticks on the y-axis |
| z_ticks | set the number of ticks on the z-axis |
| legend_text_size | size of legend |
| show_plot | show plot |
| return_plot | return ggplot object |
| save_plot | directly save the plot [boolean] |
| save_param | list of saving parameters, see |
| default_save_name | default save name for saving, don't change, change save_name in save_param |
plotly
Description of parameters.
Other spatial and dimension reduction visualizations:
spatDimPlot2D(),
spatDimPlot()