marker_surface_plot — marker_surface

Generates a 3D surface plot of the level of the selected marker. Note that the image is blurred based on the 'num_splits' parameter.

Usage

marker_surface_plot(
  sce_object,
  num_splits,
  marker,
  x_position_min = NULL,
  x_position_max = NULL,
  y_position_min = NULL,
  y_position_max = NULL
)

Arguments

sce_object: SingleCellExperiment object in the form of the output of format_image_to_sce.
num_splits: Integer specifying the number of splits on the image, higher splits equal to higher resolution. Recommendation: 10-100
marker: Marker to plot
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(SPIAT::simulated_image, num_splits=15, marker="Immune_marker1")