marker_surface_plot

Source: R/marker_surface_plot.R

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

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::formatted_image, num_splits=15, marker="CD3")