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

In dputhier/scigenex: The scigenex package (Single-Cell Informative GENe Explorer)

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

Description

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

Usage

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")
load_example_dataset("7870305/files/lymph_node_tiny_clusters_2")
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)
p + hull
p <- plot_spatial(lymph_node_tiny_2, metadata = "Cluster3", pt_size = 5)
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")
p + hull

dputhier/scigenex documentation built on May 31, 2024, 8:59 a.m.