dimPlot3D#

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Last Updated: Mar 11, 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#

`gobject`	giotto object
`spat_unit`	spatial unit
`feat_type`	feature type
`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()