plotPCA_3D#

Last Updated: Jan 14, 2025

Description#

Visualize cells according to 3D PCA dimension reduction

plotPCA_3D(
  gobject,
  dim_reduction_name = "pca",
  default_save_name = "PCA_3D",
  ...
)

`gobject`	giotto object
`dim_reduction_name`	name of PCA
`default_save_name`	default save name of PCA 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`

Description of parameters.

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