Visualize Cells And Gene Expression In A Virtual Cross Section

insertCrossSectionGenePlot3D()

Visualize cells and gene expression in a virtual cross section according to spatial coordinates.

insertCrossSectionGenePlot3D(
    gobject,
    crossSection_obj = NULL,
    name = NULL,
    spatial_network_name = "Delaunay_network",
    mesh_grid_color = "#1f77b4",
    mesh_grid_width = 3,
    mesh_grid_style = "dot",
    sdimx = "sdimx",
    sdimy = "sdimy",
    sdimz = "sdimz",
    show_other_cells = F,
    axis_scale = c("cube", "real", "custom"),
    custom_ratio = NULL,
    show_plot = NA,
    return_plot = NA,
    save_plot = NA,
    save_param = list(),
    default_save_name = "spatGenePlot3D_with_cross_section",
    ...
)

Arguments

gobject	giotto object
crossSection_obj	cross section object as alternative input. default = NULL.
name	name of virtual cross section to use
spatial_network_name	name of spatial network to use
mesh_grid_color	color for the meshgrid lines
mesh_grid_width	width for the meshgrid lines
mesh_grid_style	style for the meshgrid lines
sdimx	x-axis dimension name (default = ‘sdimx’)
sdimy	y-axis dimension name (default = ‘sdimy’)
sdimz	z-axis dimension name (default = ‘sdimy’)
show_other_cells	display not selected cells
axis_scale	axis_scale
custom_ratio	custom_ratio
show_plot	show plots
return_plot	return ggplot object
save_plot	directly save the plot [boolean]
save_param	list of saving parameters from all_plots_save_function()
default_save_name	default save name for saving, don’t change, change save_name in save_param
…	parameters for spatGenePlot3D()

Value

A ggplot.

Details

Description of parameters …