dimPlot3D#
Last Updated: Nov 17, 2023
Description#
Visualize cells according to dimension reduction coordinates
Usage#
dimPlot3D(
gobject,
spat_unit = NULL,
feat_type = NULL,
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#
|
giotto object |
|
spatial unit |
|
feature type |
|
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 |
|
names of spatial enrichment results to include |
|
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 |
|
show underlying NN network |
|
type of NN network to use (kNN vs sNN) |
|
name of NN network to use, if show_NN_network = TRUE |
|
convert color column to factor |
|
color for cells (see details) |
|
named vector with colors |
|
plot center of selected clusters |
|
plot label of selected clusters |
|
size of center points |
|
size of labels |
|
column to use for alpha of the edges |
|
size of point (cell) |
|
show plot |
|
return ggplot object |
|
directly save the plot [boolean] |
|
list of saving parameters, see
|
|
default save name for saving, don’t change, change save_name in save_param |
Details#
Description of parameters.
Value#
plotly
See Also#
Other reduced dimension visualizations: dimPlot2D()
, dimPlot()
,
plotPCA_2D()
, plotPCA_3D()
, plotPCA()
, plotTSNE_2D()
,
plotTSNE_3D()
, plotTSNE()
, plotUMAP_2D()
, plotUMAP_3D()
,
plotUMAP()