marker_surface_plot_stack: marker_surface_plot_stack

In TrigosTeam/SPIAT: Spatial Image Analysis of Tissues

marker_surface_plot_stack

Description

Generates stacked 3D surface plots showing normalized intensity level of specified markers.

Usage

marker_surface_plot_stack(
  spe_object,
  num_splits,
  markers_to_plot,
  sep = 1,
  x_position_min = NULL,
  x_position_max = NULL,
  y_position_min = NULL,
  y_position_max = NULL
)

Arguments

spe_object	SpatialExperiment object in the form of the output of format_image_to_spe.
num_splits	Integer specifying the number of splits on the image, higher splits equal to higher resolution. Recommendation: 10-100.
markers_to_plot	Vector of marker names for plotting.
sep	Integer specifying the distance separation between each surface plot. We recommend values in the 1-2 range.
x_position_min	Integer specifying the minimum x boundary to be splitted.
x_position_max	Integer specifying the maximum x boundary to be splitted.
y_position_min	Integer specifying the minimum y boundary to be splitted.
y_position_max	Integer specifying the maximum y boundary to be splitted.

Value

A plot is returned

Examples

marker_surface_plot_stack(SPIAT::simulated_image, num_splits=15, 
markers=c("Tumour_marker", "Immune_marker4"))

TrigosTeam/SPIAT documentation built on Aug. 22, 2024, 7:50 p.m.