Visualize Cells By Spatial Coordinates in 3D¶

dimPlot3D()

Visualize cells according to dimension reduction coordinates.

dimPlot3D(
    gobject,
    dim_reduction_to_use = "umap",
    dim_reduction_name = "umap",
    dim1_to_use = 1,
    dim2_to_use = 2,
    dim3_to_use = 3,
    spat_enr_names = NULL,
    select_cell_groups = NULL,
    select_cells = NULL,
    show_other_cells = T,
    other_cell_color = "lightgrey",
    other_point_size = 2,
    show_NN_network = F,
    nn_network_to_use = "sNN",
    network_name = "sNN.pca",
    color_as_factor = T,
    cell_color = NULL,
    cell_color_code = NULL,
    show_cluster_center = F,
    show_center_label = T,
    center_point_size = 4,
    label_size = 4,
    edge_alpha = NULL,
    point_size = 3,
    show_plot = NA,
    return_plot = NA,
    save_plot = NA,
    save_param = list(),
    default_save_name = "dim3D"
)

Arguments¶

gobject	giotto object
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
spat_enr_names	names of spatial enrichment results to include
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
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
color_as_factor	convert color column to factor
cell_color	color for cells (see details)
cell_color_code	named vector with colors
show_cluster_center	plot center of selected clusters
show_center_label	plot label of selected clusters
center_point_size	size of center points
label_size	size of labels
edge_alpha	column to use for alpha of the edges
point_size	size of point (cell)
show_plot	show plot
return_plot	return ggplot object
save_plot	directly save the plot [boolean]
save_param	list of saving parameters, see showSaveParameters()
default_save_name	default save name for saving, don’t change, change `save_name` in `save_param`

Value¶

A plotly.

Details¶

Description of parameters …

See dimPlot2D() and dimPlot3D() for 3D plot information.

Examples¶

dimPlot(gobjeect)