Add tissue section variable to coordinate data.frame — add_dbscan

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).

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")