`spatGenePlot3D`¶

spatGenePlot3D

Description¶

Visualize cells and gene expression according to spatial coordinates

Usage¶

spatGenePlot3D(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  genes,
  show_network = FALSE,
  network_color = NULL,
  spatial_network_name = "Delaunay_network",
  edge_alpha = NULL,
  cluster_column = NULL,
  select_cell_groups = NULL,
  select_cells = NULL,
  show_other_cells = T,
  other_cell_color = "lightgrey",
  other_point_size = 1,
  genes_high_color = NULL,
  genes_mid_color = "white",
  genes_low_color = "blue",
  show_grid = FALSE,
  spatial_grid_name = "spatial_grid",
  point_size = 2,
  show_legend = TRUE,
  axis_scale = c("cube", "real", "custom"),
  custom_ratio = NULL,
  x_ticks = NULL,
  y_ticks = NULL,
  z_ticks = NULL,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "spatGenePlot3D"
)

Arguments¶

Argument	Description
`gobject`	giotto object
`expression_values`	gene expression values to use
`genes`	genes to show
`show_network`	show underlying spatial network
`network_color`	color of spatial network
`spatial_network_name`	name of spatial network to use
`edge_alpha`	alpha of edges
`cluster_column`	cluster column to select groups
`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
`genes_high_color`	color represents high gene expression
`genes_mid_color`	color represents middle gene expression
`genes_low_color`	color represents low gene expression
`show_grid`	show spatial grid
`spatial_grid_name`	name of spatial grid to use
`point_size`	size of point (cell)
`show_legend`	show legend
`axis_scale`	the way to scale the axis
`custom_ratio`	customize the scale of the plot
`x_ticks`	set the number of ticks on the x-axis
`y_ticks`	set the number of ticks on the y-axis
`z_ticks`	set the number of ticks on the z-axis
`show_plot`	show plots
`return_plot`	return ggplot object
`save_plot`	directly save the plot [boolean]
`save_param`	list of saving parameters, see ``showSaveParameters` <#showsaveparameters>`_
`default_save_name`	default save name for saving, don’t change, change save_name in save_param

Details¶

Description of parameters.

Value¶

ggplot

Seealso¶

Other spatial gene expression visualizations:: ``spatGenePlot2D` <#spatgeneplot2d>`_ , ``spatGenePlot` <#spatgeneplot>`_