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
Examples
marker_surface_plot(SPIAT::simulated_image, num_splits=15, marker="Immune_marker1")