Visualize Cells By Spatial and Dimensional Coordinates in 3D¶

spatGenePlot3D()

Visualize cells 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¶

A ggplot.

Details¶

Description of parameters.