Generates stacked 3D surface plots showing normalized intensity level of specified markers.
Usage
marker_surface_plot_stack(
sce_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
- 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.
- 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.
Examples
marker_surface_plot_stack(SPIAT::simulated_image, num_splits=15,
markers=c("Tumour_marker", "Immune_marker4"))