spatGenePlot3D

Visualize cells and gene expression according to spatial coordinates

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

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
default_save_name	default save name for saving, don't change, change save_name in save_param

Value

ggplot

Details

Description of parameters.

See also

Other spatial gene expression visualizations: spatGenePlot2D(), spatGenePlot()