debugs

store the terminal_state in metadata so that the function downstream could retrieve it when needed.

NAMESPACE

@@ -13,8 +13,10 @@ importFrom(Matrix,solve)
 importFrom(Matrix,sparseMatrix)
 importFrom(Matrix,summary)
 importFrom(Matrix,t)
+importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,SimpleList)
+importFrom(S4Vectors,metadata)
 importFrom(SummarizedExperiment,"colData<-")
 importFrom(bluster,makeKNNGraph)
 importFrom(destiny,eigenvalues)

R/markovProbability.R

@@ -54,7 +54,7 @@
 #' @include projectProbability.R
 #' @import SingleCellExperiment
 #' @importFrom rlang abort
-#' @importFrom S4Vectors DataFrame
+#' @importFrom S4Vectors DataFrame metadata metadata<-
 #' @importFrom SummarizedExperiment colData<-
 #' @export
 markovProbability <- function(
@@ -123,5 +123,6 @@ markovProbability <- function(
         }
     } # nocov end
     colData(milo) <- cbind(colData(milo), new_coldata)
+    metadata(milo) <- c(metadata(milo), list(branch.tips = terminal_state))
     return(milo)
 }

R/projectPseudotimeToCell.R

@@ -59,8 +59,18 @@
 #' @import miloR
 #' @import SingleCellExperiment
 #' @importFrom SummarizedExperiment colData<-
+#' @importFrom S4Vectors metadata
 #' @export
-projectPseudotimeToCell <- function(milo, pb_milo, term_states, pseudotime_key = "pseudotime", suffix = "") {
+projectPseudotimeToCell <- function(milo, pb_milo, term_states = NULL, pseudotime_key = "pseudotime", suffix = "") {
+    if(is.null(term_states))
+    {
+      if(is.null(metadata(pb_milo)$branch.tips))
+      {
+        abort("Parameter Error: Please provide term_state, which should align with parameter terminal_state in function markovProbability")
+      }
+      else
+        term_states <- metadata(pb_milo)$branch.tips
+    }
     nhood <- nhoods(pb_milo) # peudobulk x cells
     # leave out cells that do not blongs to any neighbourhood
     nhoodsum <- apply(nhoods(pb_milo), 2, sum)