stratify_seurat: Given two spot groups, compute for each spot: (i) the...

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

Given two spot groups, compute for each spot: (i) the distance of the closest spot in the other class.

Description

Given two spot groups, compute for each spot: (i) the distance of the closest spot in the other class.

Usage

stratify_seurat(
  seurat_obj,
  ident = NULL,
  colours = NULL,
  colours_stratum = NULL,
  pt_size = 4,
  breaks = 5,
  labels = NULL,
  diagnostic_plot = TRUE
)

Arguments

seurat_obj	A Seurat object.
ident	The classes of the spots (0/1). A named vector (name = spot name; value = classes).
colours	Colors for the spot classes.
colours_stratum	A set of colors for the stratum.
pt_size	The size of the points.
breaks	Either a numeric vector of two or more unique cut points or a single number (greater than or equal to 2) giving the number of stratums in which spot are to be cut.
labels	Labels for the levels of the stratum. By default, labels are constructed using "(a,b]" interval notation. If labels = FALSE, simple integer codes are returned instead of a factor.
diagnostic_plot	Whether to produce a diagnostic diagram. Highly recommanded to visually inspect the results.

Examples

library(Seurat)
library(ggplot2)
load_example_dataset("7870305/files/lymph_node_tiny_2")
Seurat::SpatialDimPlot(lymph_node_tiny_2)
identity <- Idents(lymph_node_tiny_2)
classes <- ifelse(Idents(lymph_node_tiny_2) == 7, 1, 0)
names(classes) <- names(identity)
h <- display_hull(lymph_node_tiny_2, ident=classes, color="black", delta=1, size_x=3.4, size_y=3)
plot_spatial(lymph_node_tiny_2, metadata = "seurat_clusters", pt_size = 6) + h
strat <- stratify_seurat(lymph_node_tiny_2, ident=classes)
strat[[1]]
strat[[2]] + ggplot2::coord_equal()
strat[[3]] + ggplot2::coord_equal()
strat[[4]] + ggplot2::coord_equal() 

dputhier/scigenex documentation built on Dec. 20, 2024, 2:22 a.m.