plotTSNE_3D#

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Last Updated: Mar 11, 2023

Description#

Visualize cells according to dimension reduction coordinates

Usage#

plotTSNE_3D(
  gobject,
  dim_reduction_name = "tsne",
  default_save_name = "TSNE_3D",
  ...
)

Arguments#

gobject

giotto object

dim_reduction_name

name of TSNE

default_save_name

default save name of TSNE plot

...

Arguments passed on to dimPlot3D

spat_unit

spatial unit

feat_type

feature type

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

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

cell_color

color for cells (see details)

color_as_factor

convert color column to factor

cell_color_code

named vector with colors

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_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

Details#

Description of parameters.

Value#

plotly

See Also#

Other reduced dimension visualizations: dimPlot2D(), dimPlot3D(), dimPlot(), plotPCA_2D(), plotPCA_3D(), plotPCA(), plotTSNE_2D(), plotTSNE(), plotUMAP_2D(), plotUMAP_3D(), plotUMAP()