dimPlot3D

dimPlot3D

Description

Visualize cells according to dimension reduction coordinates

Usage

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

Argument	Description
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` <#showsaveparameters>`_
default_save_name	default save name for saving, don’t change, change save_name in save_param

Details

Description of parameters.

Value

plotly

Seealso

Other reduced dimension visualizations:

``dimPlot2D` <#dimplot2d>`_ , ``dimPlot` <#dimplot>`_ , ``plotPCA_2D` <#plotpca2d>`_ , ``plotPCA_3D` <#plotpca3d>`_ , ``plotPCA` <#plotpca>`_ , ``plotTSNE_2D` <#plottsne2d>`_ , ``plotTSNE_3D` <#plottsne3d>`_ , ``plotTSNE` <#plottsne>`_ , ``plotUMAP_2D` <#plotumap2d>`_ , ``plotUMAP_3D` <#plotumap3d>`_ , ``plotUMAP` <#plotumap>`_