Add holes to spatial annotations

These methods allow the addition of an inner border to spatial annotations, creating holes.

addInnerBorder(object, ...)

# S4 method for class 'SPATA2'
addInnerBorder(object, id, border_df, new_id = FALSE, overwrite = FALSE, ...)

# S4 method for class 'SpatialAnnotation'
addInnerBorder(object, border_df, ...)

Arguments

object

An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.

...

Used to absorb deprecated arguments or functions.

id

Character value. The ID of the spatial annotation to which the hole is added.

border_df

A data.frame that contains the x- and y- positions of the vertices of the polygon that corresponds to the borders of the whole. See details for input requirements.

new_id

If character value, stores the resulting spatial annotatiton under the specified ID.

overwrite

Logical value. Must be TRUE to allow overwriting.

Value

The updated input object, containing the added, removed or computed results.

Details

If used on a SpatialAnnotation directly, the variables of border_df should be called x_orig and y_orig and should be scaled correspondingly. If used with the SPATA2 object, the variables can be called x and y, too. In that case, the function assumes that the coordinates are scaled to the image that is currently active and creates x_orig and y_orig accordingly.

Examples


library(SPATA2)
library(tidyverse)

data("example_data")

object <- example_data$object_UKF275T_diet

create_circle_polygon <- function(p, r, n) {

 angles <- seq(0, 2 * pi, length.out = n + 1)

 x_coords <- p[1] + r * cos(angles)
 y_coords <- p[2] + r * sin(angles)

 polygon_df <- tibble::tibble(x = x_coords, y = y_coords)

 return(polygon_df)

}

center <-
 getCoordsDf(object)[c("x", "y")] %>%
 map_dbl(.f = mean)

area_circle <- create_circle_polygon(center, r = 75, n = 100)

print(area_circle)

object <- addSpatialAnnotation(object, area = list(outer = area_circle), id = "circle")

plotSpatialAnnotations(object, ids = "circle")

hole <- create_circle_polygon(center, r = 25, n = 100)

object <- addInnerBorder(object, id = "circle", border_df = hole, new_id = "circle_with_hole")

plotSpatialAnnotations(object, ids = c("circle", "circle_with_hole"))