dimPlot3D: dimPlot3D

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

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

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

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()

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.