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marker_surface_plot_stack

Source: R/marker_surface_plot_stack.R
marker_surface_plot_stack.Rd

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.

Value

A plot is returned

Examples

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