draw polygon / path with holes

[tdhock]

this is apparently possible with d3 https://devdocs.io/d3~3/geo-paths.md#_path

and it can be done with R grid / isoband

# shape with hole
m <- matrix(c(0, 0, 0, 0, 0, 0,
              0, 1, 1, 1, 1, 0,
              0, 1, 0, 0, 1, 0,
              0, 1, 0, 0, 1, 0,
              0, 1, 1, 1, 1, 0,
              0, 0, 0, 0, 0, 0), 6, 6, byrow = TRUE)
isoband::plot_iso(m, 0.5, 1.5)

this animint code gives two filled polygons instead of one with a hole.

res=isoband::isobands((1:ncol(m))/(ncol(m)+1), (nrow(m):1)/(nrow(m)+1), m, 0.5, 1.5)[[1]]
## ?grid.path
##     rule: A character value specifying the fill rule: either
##           ‘"winding"’ or ‘"evenodd"’.
## A path is like a polygon except that the former can contain holes,
## as interpreted by the fill rule; these fill a region if the path
## border encircles it an odd or non-zero number of times,
## respectively.
viz <- animint(poly=ggplot()+
  geom_polygon(aes(
    x, y, group=id, fill=ID),
    data=as.data.table(res)[, ID := factor(id)]))
viz$poly
viz

> res
$x
 [1] 0.7142857 0.5714286 0.4285714 0.2857143 0.2142857 0.2142857 0.2142857 0.2142857 0.2857143
[10] 0.4285714 0.5714286 0.7142857 0.7857143 0.7857143 0.7857143 0.7857143 0.5714286 0.6428571
[19] 0.6428571 0.5714286 0.4285714 0.3571429 0.3571429 0.4285714

$y
 [1] 0.2142857 0.2142857 0.2142857 0.2142857 0.2857143 0.4285714 0.5714286 0.7142857 0.7857143
[10] 0.7857143 0.7857143 0.7857143 0.7142857 0.5714286 0.4285714 0.2857143 0.3571429 0.4285714
[19] 0.5714286 0.6428571 0.6428571 0.5714286 0.4285714 0.3571429

$id
 [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2

[tdhock]

real data application is for Hi-C clusters, below we see

• left 0/1 heat map of data input to contouring algo
• correct drawing with holes using isobands::plot_iso().

code from https://github.com/tdhock/hicream-viz/blob/main/data-2025-10-09/figure-pixels-chr1-Cluster73-debug.R

above we see

• left polygons from contourLines()
• right polygons from isoband::isobands()

both incorrectly show hole as another filled polygon (holes should not be filled)

[tdhock]

https://r-spatial.github.io/sf/articles/sf1.html says "POLYGON geometry with a positive area (two-dimensional); sequence of points form a closed, non-self intersecting ring; the first ring denotes the exterior ring, zero or more subsequent rings denote holes in this exterior ring"

[tdhock]

this is supported in ggplot2 as of 2019 https://tidyverse.org/blog/2019/06/ggplot2-3-2-0/#new-features
Much as the group aesthetic separates polygons in the data, the subgroup aesthetic separates parts of each polygon. The first occurring subgroup should always be the outer ring of the polygon and any subsequent subgroup will describe holes in this (or, potentially, polygons within the holes and so on).
see code and output here https://github.com/tdhock/hicream-viz?tab=readme-ov-file#14-oct-2025

[tdhock]

this is more complex but not necessary to support for the hic data application

m <- rbind(
  c(0, 0, 0, 0, 0, 0, 0),
  c(0, 1, 1, 1, 1, 1, 0),
  c(0, 1, 0, 0, 0, 1, 0),
  c(0, 1, 0, 1, 0, 1, 0),
  c(0, 1, 0, 0, 0, 1, 0),
  c(0, 1, 1, 1, 1, 1, 0),
  c(0, 0, 0, 0, 0, 0, 0))
isoband::plot_iso(m, 0.5, 1.5)
iband <- isoband::isobands((1:ncol(m))/(ncol(m)+1), (nrow(m):1)/(nrow(m)+1), m, 0.5, 1.5)[[1]]
library(data.table)
idt <- as.data.table(iband)[, ID := factor(id)]
library(ggplot2)
ggplot()+
  geom_polygon(aes(
    x, y, group=1, subgroup=id),
    data=idt)

test case should involve clickID() or mouseMove().

[tdhock]

more complete test case

m_list <- list(
  hole_and_mid=rbind(
    c(0, 0, 0, 0, 0, 0, 0),
    c(0, 1, 1, 1, 1, 1, 0),
    c(0, 1, 0, 0, 0, 1, 0),
    c(0, 1, 0, 1, 0, 1, 0),
    c(0, 1, 0, 0, 0, 1, 0),
    c(0, 1, 1, 1, 1, 1, 0),
    c(0, 0, 0, 0, 0, 0, 0)),
  only_hole=rbind(
    c(0, 0, 0, 0, 0, 0, 0),
    c(0, 1, 1, 1, 1, 1, 0),
    c(0, 1, 0, 0, 0, 1, 0),
    c(0, 1, 0, 0, 0, 1, 0),
    c(0, 1, 0, 0, 0, 1, 0),
    c(0, 1, 1, 1, 1, 1, 0),
    c(0, 0, 0, 0, 0, 0, 0)),
  no_hole=rbind(
    c(0, 0, 0, 0, 0, 0, 0),
    c(0, 1, 1, 1, 1, 1, 0),
    c(0, 1, 1, 1, 1, 1, 0),
    c(0, 1, 1, 1, 1, 1, 0),
    c(0, 1, 1, 1, 1, 1, 0),
    c(0, 1, 1, 1, 1, 1, 0),
    c(0, 0, 0, 0, 0, 0, 0)))    
isoband::plot_iso(m_list$hole_and_mid, 0.5, 1.5)

library(data.table)
two <- function(x,label)data.table(
  x=x+offset, y=c(3,5),
  label=sprintf(
    "%s_%s_%s", grp, label,c("bottom","top")))
point_dt_list <- list()
polygon_dt_list <- list()
for(grp.i in seq_along(m_list)){
  offset <- grp.i*10
  grp <- names(m_list)[[grp.i]]
  point_dt_list[[grp.i]] <- rbind(
    two(4, "mid"),
    two(5, "hole"),
    two(6, "ring"),
    two(7, "out"))
  m <- m_list[[grp.i]]
  iband <- isoband::isobands(1:ncol(m), nrow(m):1, m, 0.5, 1.5)[[1]]
  polygon_dt_list[[grp.i]] <- as.data.table(iband)[, let(
    grp = grp,
    x=x+offset)]
}
polygon_dt <- rbindlist(polygon_dt_list)
point_dt <- rbindlist(point_dt_list)
library(ggplot2)
ggplot()+
  geom_polygon(aes(
    x, y, group=grp, subgroup=id),
    data=polygon_dt)+
  geom_text(aes(
    x-0.5,y,label=label),
    color="red",
    size=5,
    hjust=0,
    angle=60,
    data=point_dt)+
  geom_point(aes(
    x,y,id=label),
    color="red",
    data=point_dt)

above ggplot2 below animint2