Subsets SpaMTP Seurat Object containing FOVs

Intermediate solution to subset(): subset FOVs/centroids if selected cells are NOT found in each FOV NOTE: some code parts and args are taken from SeuratObject

Usage

subset_SPM(
  object = NULL,
  subset = NULL,
  cells = NULL,
  idents = NULL,
  features = NULL,
  Update.slots = TRUE,
  Update.object = TRUE,
  verbose = FALSE,
  ...
)

Arguments

object: An S4 object or A FOV object
subset: Logical expression indicating features/variables to keep
cells: A vector of cells to keep; if NULL, defaults to all cells
idents: A vector of identity classes to keep
features: A vector of feature names or indices to keep
Update.slots: If to update slots of an object
Update.object: If to update final object, default to TRUE.
verbose: Boolean indicating whether to show the message. If TRUE the message will be show, else the message will be suppressed (default = FALSE).
...: Arguments passed to subset() and other methods

Value

A subset Seurat object

Details

Function params/args:

Examples

utils::str(formals(subset_SPM))
#> Dotted pair list of 9
#>  $ object       : NULL
#>  $ subset       : NULL
#>  $ cells        : NULL
#>  $ idents       : NULL
#>  $ features     : NULL
#>  $ Update.slots : logi TRUE
#>  $ Update.object: logi TRUE
#>  $ verbose      : logi FALSE
#>  $ ...          : symbol 
# sub <- subset_obt(seurat.obj, idents = "Sample1")