plotUMAP_3D: plotUMAP_3D

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

plotUMAP_3D

Description

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 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_3D(), plotTSNE(), plotUMAP_2D(), plotUMAP()

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.