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"
)
giotto object
direction to align plot
dimension reduction to use
dimension reduction name
dimension to use on x-axis
dimension to use on y-axis
dimension to use on z-axis
= spatial dimension to use on x-axis
= spatial dimension to use on y-axis
= spatial dimension to use on z-axis
names of spatial enrichment results to include
show underlying NN network
type of NN network to use (kNN vs sNN)
name of NN network to use, if show_NN_network = TRUE
color of nn network
column to use for alpha of the edges
show the center of each cluster
provide a label for each cluster
size of the center point
size of the center label
select subset of cells/clusters based on cell_color parameter
select subset of cells based on cell IDs
display not selected cells
color of not selected cells
size of not selected cells
color for cells (see details)
convert color column to factor
named vector with colors
size of points in dim. reduction space
show spatial network
name of spatial network to use
color of spatial network
alpha of spatial network
show spatial grid
name of spatial grid to use
color of spatial grid
alpha of spatial grid
size of spatial points
the way to scale the axis
customize the scale of the plot
set the number of ticks on the x-axis
set the number of ticks on the y-axis
set the number of ticks on the z-axis
size of legend
show plot
return ggplot object
directly save the plot [boolean]
list of saving parameters, see showSaveParameters
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()