Merge branch 'issue-46' into dev

* issue-46:
  Increment version number to 1.2.3.9001
  🐞 Fix: update docs
  🐞 Fix: DRY code

Author: wleoncio

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: DIscBIO
 Date: 2026-01-08
 Title: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics
-Version: 1.2.3.9000
+Version: 1.2.3.9001
 Authors@R:
   c(
     person(

NAMESPACE

@@ -91,15 +91,13 @@ importFrom(httr,status_code)
 importFrom(igraph,E)
 importFrom(igraph,V)
 importFrom(igraph,as_adjacency_matrix)
-importFrom(igraph,mean_distance)
 importFrom(igraph,betweenness)
 importFrom(igraph,degree)
 importFrom(igraph,distance_table)
-importFrom(igraph,as_adjacency_matrix)
 importFrom(igraph,get.edgelist)
 importFrom(igraph,get.shortest.paths)
-importFrom(igraph,graph_from_data_frame)
 importFrom(igraph,graph_from_adjacency_matrix)
+importFrom(igraph,graph_from_data_frame)
 importFrom(igraph,mean_distance)
 importFrom(igraph,mst)
 importFrom(impute,impute.knn)

R/DIscBIO-generic-clusteringOrder.R

@@ -6,7 +6,6 @@
 #' @param quiet if `TRUE`, suppresses intermediary output
 #' @param export if `TRUE`, exports order table to csv
 #' @param filename Name of the exported file (if `export=TRUE`)
-#' @importFrom TSCAN TSCANorder
 #' @note This function has been replaced by pseudoTimeOrdering(), but it is
 #'   being kept for legacy purposes. It will, however, be removed from future
 #'   versions of DIscBIO.
@@ -19,6 +18,7 @@ setGeneric("KmeanOrder", function(
 
 #' @export
 #' @rdname KmeanOrder
+#' @importFrom TSCAN TSCANorder
 setMethod(
   "KmeanOrder",
   signature = "DISCBIO",
@@ -31,6 +31,7 @@ setMethod(
       "but will be removed in future versions of DIscBIO. ",
       "Please adapt your scripts accordingly."
     )
+
     # Validation
     if (length(object@kmeans$kpart) == 0) {
       stop("run Clustexp before KmeanOrder")

R/DIscBIO-generic-pseudoTimeOrdering.R

@@ -6,7 +6,6 @@
 #' @param quiet if `TRUE`, suppresses intermediary output
 #' @param export if `TRUE`, exports order table to csv
 #' @param filename Name of the exported file (if `export=TRUE`)
-#' @importFrom TSCAN TSCANorder
 #' @return The DISCBIO-class object input with the kordering slot filled.
 setGeneric("pseudoTimeOrdering", function(
     object,
@@ -18,6 +17,7 @@ setGeneric("pseudoTimeOrdering", function(
 
 #' @export
 #' @rdname pseudoTimeOrdering
+#' @importFrom TSCAN TSCANorder
 setMethod(
   "pseudoTimeOrdering",
   signature = "DISCBIO",
@@ -31,15 +31,15 @@ setMethod(
       Obj <- object@fdata
       Names <- object@cpart
       lpsmclust <- Exprmclust(Obj, K = 4, reduce = FALSE, cluster = Names)
-      lpsorder <- TSCANorder(lpsmclust)
     } else if (ran_m) {
       Obj <- object@fdata
       Names <- names(object@MBclusters$clusterid)
       lpsmclust <- object@MBclusters
-      lpsorder <- TSCANorder(lpsmclust)
     } else {
       stop("run clustexp before this pseudoTimeOrdering")
     }
+    lpsorder <- TSCANorder(lpsmclust)
+
     # ======================================================================
     # Ordering
     # ======================================================================