plotUMAP_3D

Visualize cells according to dimension reduction coordinates

Usage

plotUMAP_3D(
  gobject,
  dim_reduction_name = "umap",
  default_save_name = "UMAP_3D",
  ...
)

Arguments

gobject

giotto object

dim_reduction_name

name of UMAP

default_save_name

default save name of UMAP plot

...

Arguments passed on to dimPlot3D

spat_unit

spatial unit (e.g. "cell")

feat_type

feature type (e.g. "rna", "dna", "protein")

show_plot

logical. show plot

return_plot

logical. return ggplot object

save_plot

logical. save the plot

save_param

list of saving parameters, see showSaveParameters

dim1_to_use

numeric. dimension to use on x-axis

dim2_to_use

numeric. dimension to use on y-axis

dim3_to_use

numeric. dimension to use on z-axis

show_NN_network

logical. Show underlying NN network

nn_network_to_use

character. type of NN network to use (kNN vs sNN)

network_name

character. name of NN network to use, if show_NN_network = TRUE

spat_enr_names

character. names of spatial enrichment results to include

cell_color

character. what to color cells by (e.g. metadata col or spatial enrichment col)

color_as_factor

logical. convert color column to factor. Discrete colors are used when this is TRUE. continuous colors when FALSE.

cell_color_code

character. discrete colors to use. palette to use or named vector of 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 for not selected cells

other_point_size

point size for 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)

Value

plotly

Details

Description of parameters.

See also

Other reduced dimension visualizations: dimPlot2D(), plotPCA(), plotPCA_2D(), plotPCA_3D(), plotTSNE(), plotTSNE_2D(), plotTSNE_3D(), plotUMAP(), plotUMAP_2D()

Examples

g <- GiottoData::loadGiottoMini("starmap")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 
#> 4. read Giotto image information
#> 
#> no external python path or giotto
#>  environment was specified, will check if a
#>  default python path is available
#> 
#> A default python path was found: /usr/bin/python3 and will be used
#>  If this is not the correct python path, either
#> 
#> 1. use installGiottoEnvironment() to install
#>  a local miniconda python environment along with required modules
#> 
#> 2. provide an existing python path to
#>  python_path to use your own python path which has all modules
#>  installed
#> Set options("giotto.use_conda" = FALSE) if
#>  python functionalities are not needed
plotUMAP_3D(g, dim_reduction_name = "3D_umap")
#> create 3D plot