Draw a hull around a region of interest of Visium data.

Draw a hull around a region of interest of Visium data.

display_hull(
  data = NULL,
  ident = NULL,
  size_x = 2.4,
  size_y = 2,
  step_x = 2.6,
  step_y = 2.4,
  delta = 0.3,
  color = "white",
  hull_type = c("walls", "ggforce"),
  expand = unit(0.05, "mm"),
  radius = unit(0.5, "mm"),
  concavity = 1,
  size = 0.7
)

Arguments

data

A Seurat spatial object (Visium technology) or a data.frame (spot coordinates).

ident

A binary vector whose length correspond to the number of columns/spots in the seurat object. 1 corresponds to the spots of the class of interest for which a hull is to be displayed

size_x

The size of the square (x axis)

size_y

The size of the square (y axis)

step_x

The distance between two points on the x axis.

step_y

The distance between two points on the y axis.

delta

Add more or less flexibility to search for neighbor points

color

A color for the hull.

hull_type

The method for drawing the hull: 'ggforce' (see ggforce::geom_mark_hull) or 'wall'. If wall, segment wont be connected but this will frequently allows to obtain a better delimited hull.

expand

For hull_type 'ggforce'. A numeric or unit vector of length one, specifying the expansion amount.

radius

For hull_type 'ggforce'. As expand but specifying the corner radius.

concavity

A measure of the concavity of the hull. 1 is very concave while it approaches convex as it grows. Defaults to 2.

size

The line width.

Value

A ggplot object (with segments).

Examples

library(Seurat)
load_example_dataset("7870305/files/lymph_node_tiny_2")
#> |-- INFO :  Dataset 7870305/files/lymph_node_tiny_2 was already loaded. 
load_example_dataset("7870305/files/lymph_node_tiny_clusters_2")
#> |-- INFO :  Dataset 7870305/files/lymph_node_tiny_clusters_2 was already loaded. 
lymph_node_tiny_2 <- Seurat::AddModuleScore(lymph_node_tiny_2, features = lymph_node_tiny_clusters_2@gene_clusters, nbin = 10)
p <- Seurat::SpatialDimPlot(lymph_node_tiny_2, pt.size.factor = 4)
p

hull <- display_hull(lymph_node_tiny_2, 
        ident=ifelse(Seurat::Idents(lymph_node_tiny_2) %in% c(7, 8), 1, 0),
        delta=1, size_x=3.4, size_y=3)
#> |-- INFO :  Creating a dataframe to store output 
#> |-- INFO :  Creating a list of neighborhoods. 
#> |-- INFO :  Looping over the points. 
p + hull

p <- plot_spatial(lymph_node_tiny_2, metadata = "Cluster3", pt_size = 5)
#> |-- INFO :  Feature is not a factor. 
hull <- display_hull(lymph_node_tiny_2, 
                     ident=ifelse(Seurat::  Idents(lymph_node_tiny_2) %in% c(7, 8), 1, 0),
                     delta=1, size_x=3.4, size_y=3, color="black")
#> |-- INFO :  Creating a dataframe to store output 
#> |-- INFO :  Creating a list of neighborhoods. 
#> |-- INFO :  Looping over the points. 
p + hull