Merge branch 'devel'

kayla-jackson · kayla-jackson · commit 06e5aa4e9972 · 2025-06-12T13:35:23.000-07:00
Include bug fixes and changes to output from `calculateConcordex()`. Also changes approach to serial evaluation
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: concordexR
 Title: Identify Spatial Homogeneous Regions with concordex
-Version: 1.9.0
+Version: 1.9.1
 Authors@R: c(
     person("Kayla", "Jackson", , "kaylajac@caltech.edu", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-6483-0108")),
@@ -31,7 +31,7 @@ URL: https://github.com/pachterlab/concordexR,
     https://pachterlab.github.io/concordexR/
 BugReports: https://github.com/pachterlab/concordexR/issues
 Depends: 
-    R (>= 4.4.0)
+    R (>= 4.5.0)
 Imports: 
     BiocGenerics,
     BiocNeighbors,
diff --git a/R/concordex-internals.R b/R/concordex-internals.R
@@ -30,21 +30,29 @@
     check_dots_empty()
     dims <- dim(g)
 
-
-    # The graph is dense, so we can get some improvements on mapping
+    # The index is dense, so we can get some improvements
     # by converting to a list of rows
-    g <- pmap(data.frame(g), c)
+    g <- split(g, seq(dims[1]))
 
-    nbc <- bplapply(g, function(rows) {
-        nbx <- colMeans2(labels, rows=rows)
-        as(nbx,"sparseMatrix")},
-    BPPARAM=BPPARAM)
+    nw <- BPPARAM$workers
 
-    nbc <- do.call(cbind, nbc)
+    .consolidate <- function(rows) {
+        mapply(FUN=function(r){colMeans2(labels, rows=r)}, rows, SIMPLIFY=FALSE)
+    }
 
-    # Transpose so that labels are on columns
-    t(nbc)
+    if (nw <= 1L) {
+        # Avoid `bplappy()` for serial
+        nbc <- .consolidate(g)
+        nbc <- do.call(rbind, nbc)
 
+    } else {
+        nbc <- bpvec(g, .consolidate,
+                 AGGREGATE = function(...) do.call(rbind, c(...)),
+                 BPPARAM=BPPARAM)
+    }
+    # Transpose so that labels are on columns
+    # t(nbc)
+    nbc
 }
 
 .concordex_stat <- function(nbc, labels, n_neighbors) {
@@ -95,23 +103,26 @@
 
     # Compute for each row(/cell/spot) in g
     nbc <- .concordex_nbhd_consolidation(g, labels, BPPARAM=BPPARAM)
+    out <- list("NBC"=nbc)
 
     if (cluster_neighborhoods & !missing(BLUSPARAM)) {
         if (class(BLUSPARAM) %in% "MbkmeansParam") {
             shr <- clusterRows(as.matrix(nbc), BLUSPARAM=BLUSPARAM)
         } else {
-           shr <- clusterRows(nbc, BLUSPARAM=BLUSPARAM)
+           shr <- clusterRows(nbc, BLUSPARAM=BLUSPARAM, full=FALSE)
         }
 
-        attr(nbc, "shrs") <- shr
+        out[['SHR']] <- shr
     }
 
     if (compute_similarity) {
         # statistics
         cdx <- .concordex_stat(nbc, labels, n_neighbors=n_neighbors)
-        attr(nbc, "similarity") <- cdx$similarity
-        attr(nbc, "concordex") <- cdx$concordex
+
+        out[["SIMILARITY"]] <- cdx$similarity
+        out[["CONCORDEX_SCORE"]] <- cdx$concordex
+
     }
 
-    nbc
+    out
 }
diff --git a/R/concordex.R b/R/concordex.R
@@ -46,8 +46,8 @@
 #'   parallelized (see \code{\link{bpparam}}).
 #'
 #' @return
-#' For \code{calculateConcordex}, a sparse, numeric matrix representing the
-#' neighborhood consolidation for each cell (row)
+#' For \code{calculateConcordex}, A list containing a sparse, numeric matrix representing the
+#' neighborhood consolidation for each cell (row) and SHR identities.
 #'
 #' For \code{runConcordex}, a SingleCellExperiment (or SpatialExperiment) object
 #' is returned containing this matrix in \code{\link{reducedDims}(..., name)}.
@@ -92,8 +92,8 @@ setMethod("calculateConcordex", "ANY",
             ...,
             n_neighbors=30,
             compute_similarity=FALSE,
-            BLUSPARAM,
             BNINDEX,
+            BLUSPARAM=NNGraphParam(cluster.fun="louvain"),
             BNPARAM=KmknnParam(),
             BPPARAM=SerialParam()) {
 
@@ -154,7 +154,7 @@ setMethod("calculateConcordex", "SummarizedExperiment",
 #' @param ... Other parameters passed to default method
 #' @param use.dimred Integer or string specifying the reduced dimensions to use
 #'   for construction of the k-nearest neighbor graph. Note that if this is not
-#'   \code{NULL}, reduced dimensions can not be used as labels to compute the
+#'   \code{NULL}, reduced dimensions cannot be used as labels to compute the
 #'   neighborhood consolidation matrix.
 #'
 #' @export
@@ -204,10 +204,10 @@ setMethod("runConcordex", "SpatialExperiment", function(x, labels, ..., name="NB
     {
     nbc <- calculateConcordex(x, labels, ...)
 
-    if ("shrs" %in% names(attrs(nbc))) {
-        colData["shr"] <- attrs(nbc)$shrs
+    if ("SHR" %in% names(nbc)) {
+        colData["shr"] <- nbc[["SHR"]]
     }
-    reducedDim(x, name) <- nbc
+    reducedDim(x, name) <- nbc[["NBC"]]
 
     x
     })
@@ -217,7 +217,7 @@ setMethod("runConcordex", "SpatialExperiment", function(x, labels, ..., name="NB
 #' @rdname calculateConcordex
 setMethod("runConcordex", "SingleCellExperiment", function(x, labels, ..., name="NBC")
 {
-    reducedDim(x, name) <- calculateConcordex(x, labels, ...)
-
+    nbc <- calculateConcordex(x, labels, ...)
+    reducedDim(x, name) <- nbc[["NBC"]]
     x
 })
diff --git a/man/calculateConcordex.Rd b/man/calculateConcordex.Rd
diff --git a/vignettes/concordex-nonspatial.Rmd b/vignettes/concordex-nonspatial.Rmd
@@ -187,7 +187,7 @@ the proportion of cells with each label in the neighborhood of other cells with
 same label.
 
 ```{r}
-sim <- attr(res, "similarity")
+sim <- res[["SIMILARITY"]]
 
 round(sim, 2)
 ```
