plotPCA_3D

Visualize cells according to 3D PCA dimension reduction

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

Arguments

gobject

giotto object

dim_reduction_name

name of PCA

default_save_name

default save name of PCA plot

...

Arguments passed on to dimPlot3D

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

plotly

Description of parameters.