Add tissue section variable — 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", ...)

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

Arguments

coords_df: Data.frame with x and y variable.
eps: size (radius) of the epsilon neighborhood. Can be omitted if x is a frNN object.
minPts: 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.
ccd: Center to center distance in pixel units.

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


# --- identify tissue sections
object <- downloadPubExample("MCI_LMU", verbose = FALSE)

coords_df <- getCoordsDf(object)

coords_df <- add_tissue_section_variable(coords_df, ccd = getCCD(object, "px"))

plotSurface(coords_df, color_by = "section")

# --- identify artefact spots
object <- SPATAData::downloadSpataObject("269_T", verbose = FALSE)

coords_df <- getCoordsDf(object)

coords_df <- add_tissue_section_variable(coords_df, ccd = getCCD(object, "px"))

plotSurface(coords_df, color_by = "section")