dimPlot3D#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_visuals.R#L7038

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#

Argument

Description

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 `showSaveP arameters <#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>`__