arrange_as_polygon: Arrange observations as polygon

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Arrange observations as polygon

Description

Arranges spatial observations by angle to the center in order to deal with them as a polygon. Works under the assumptions that observations are vertices of a polygon and that the outline of the tissue section is roughly circular.

Usage

arrange_as_polygon(input_df, use = "angle")

Arguments

input_df

Data.frame with at least two numeric variables named x and y.

Examples

 library(tidyverse)

 object <- downloadPubExample("313_T")

 pt_size <- getDefault(object, "pt_size")

 outline_df <- getTissueOutlineDf(object, remove = FALSE)

 print(outline_df)

 plotSurface(outline_df, color_by = "outline")

 outline_only <- filter(outline_df, outline)

 print(outline_only)

 plotSurface(object) +
  geom_point_fixed(data = outline_only, mapping = aes(x = x, y = y), color = "red", size = pt_size)

 # fails due to inadequate sorting of observations
 plotSurface(object) +
  geom_polygon(data = outline_only, mapping = aes(x = x, y = y), color = "red", alpha = 0.4)

 # calculate (and arrange by) angle to center
 outline_only_arr <- arrange_as_polygon(input_df = outline_only)

 plotSurface(object) +
  geom_point_fixed(
   data = outline_only_arr,
   mapping = aes(x = x, y = y, color = atc),
   size = pt_size
   )

 # works
 plotSurface(object) +
  geom_polygon(data = outline_only_arr, mapping = aes(x = x, y = y), color = "red", alpha = 0.4)

theMILOlab/SPATA2 documentation built on June 1, 2025, 9:11 p.m.