Obtain outline barcode spots

Identifies the barcode spots that lie on the edge of the tissue and returns a subset of the coordinates data.frame. Requires the results of identifyTissueOutline().

getTissueOutlineDf(object, remove = TRUE)

Arguments

object

An object of class spata2.

remove

Logical. If TRUE, none-outline spots are removed from the output.

force

Logical. If TRUE, forces computation.

Value

Output of getCoordsDf() filtered based on the outline variable.

Examples

 library(ggplot2)
 library(ggExtra)

 object <- downloadPubExample("MCI_LMU")

 print(getTissueOutlineDf(object))

 to_df <- getTissueOutlineDf(object, remove = FALSE)

 to_df[["outline"]] <- as.character(to_df[["outline"]])

 ggplot(to_df, mapping = aes(x = x, y = y)) +
   geom_point_fixed(mapping = aes(color = section, alpha = outline), size = getDefault(object, "pt_size")) +
   scale_alpha_manual(values = c("TRUE" = 1, "FALSE" = 0.4))