add_dbscan_variable: Add tissue section variable to coordinate data.frame

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Add tissue section variable to coordinate data.frame

Description

Leverages dbscan::dbscan() to identify tissue sections on the slide and to group barcode spots accordingly. Required to approximate the outline of the tissue section(s).

Usage

add_dbscan_variable(
  coords_df,
  eps,
  minPts = 3,
  name = "dbscan",
  x = "x",
  y = "y",
  min_cluster_size = 1,
  ...
)

add_tissue_section_variable(coords_df, ccd, minPts = 3, ...)

Arguments

coords_df	Data.frame with x and y variable.
eps	Distance measure. Given to eps of dbscan::dbscan(). Determines the size (radius) of the epsilon neighborhood.
minPts	Numeric value. Given to dbscan::dbscan(). Determines the number of minimum points required in the eps neighborhood for core points (including the point itself)
name	Name of the added variable.
...	To silently drop deprecated arguments.

Value

Data.frame with additional variable containing numbers. 0 means that the spot is not connected to any other spot (probably artefact). 1-n corresponds to the tissue sections.

Note

add_dbscan_variable() is the working horse. add_tissue_section_variable() has specific defaults.

Examples

library(SPATA2)
library(EBImage)
library(tidyverse)

data("example_data")

object <- example_data$object_LMU_MCI_diet

coords_df <-
 getCoordsDf(object) %>%
 add_dbscan_variable(eps = recDbscanEps(object), name = "section")

plotSurface(coords_df, color_by = "section")

theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.