splitComponent #73

Author: lambdamoses

NAMESPACE

@@ -149,6 +149,7 @@ export(spatialGraph)
 export(spatialGraphNames)
 export(spatialGraphs)
 export(splitByCol)
+export(splitComponent)
 export(splitContiguity)
 export(splitSamples)
 export(spotPoly)
@@ -265,6 +266,7 @@ importFrom(S4Vectors,mcols)
 importFrom(S4Vectors,metadata)
 importFrom(S4Vectors,setValidity2)
 importFrom(S4Vectors,showAsCell)
+importFrom(S4Vectors,split)
 importFrom(SingleCellExperiment,"altExp<-")
 importFrom(SingleCellExperiment,"int_colData<-")
 importFrom(SingleCellExperiment,"int_elementMetadata<-")
@@ -389,6 +391,7 @@ importFrom(spdep,graph2nb)
 importFrom(spdep,knearneigh)
 importFrom(spdep,knn2nb)
 importFrom(spdep,mat2listw)
+importFrom(spdep,n.comp.nb)
 importFrom(spdep,nb2listw)
 importFrom(spdep,nb2listwdist)
 importFrom(spdep,poly2nb)

R/spatialGraphs.R

@@ -14,7 +14,10 @@
 #' Spatial neighborhood graphs as \code{spdep}'s \code{listw} objects are stored
 #' in the \code{int_metadata} of the SFE object. The \code{listw} class is used
 #' because \code{spdep} has many useful methods that rely on the neighborhood
-#' graph as \code{listw}.
+#' graph as \code{listw}. See the
+#' \href{https://r-spatial.github.io/spdep/reference/index.html}{\code{spdep}
+#' doumentation website} for functions to edit the spatial neighborhood graph,
+#' or the \code{nb} object within the \code{listw}.
 #'
 #' @param x A \code{SpatialFeatureExperiment} object.
 #' @param value A \code{listw} object (\code{*Graph}), or a named list of list
@@ -38,9 +41,9 @@
 #'   argument in \code{\link[SpatialExperiment]{SpatialExperiment}}.
 #' @name spatialGraphs
 #' @concept Getters and setters
-#' @return Getters for multiple graphs return a named list. Getters for
-#'   names return a character vector of the names. Getters for single graphs
-#'   return a \code{listw} object. Setters return an SFE object.
+#' @return Getters for multiple graphs return a named list. Getters for names
+#'   return a character vector of the names. Getters for single graphs return a
+#'   \code{listw} object. Setters return an SFE object.
 #' @aliases rowGraphs rowGraphs<- spatialGraph spatialGraph<- spatialGraphNames
 #'   colGraphs colGraphs<- spatialGraphNames<- spatialGraphs<- annotGraphs
 #'   annotGraphs<-

R/split.R

@@ -8,6 +8,9 @@
 #' SFE object by \code{sample_id} so each sample will become a separate SFE
 #' object. The \code{splitContiguity} function splits the SFE object by
 #' contiguity of an \code{annotGeometry}, which by default is "tissueBoundary".
+#' The \code{splitComponent} function splits the SFE object by graph component,
+#' so if there are disconnected components in the graph, then each component 
+#' will become a new SFE object.
 #'
 #' @inheritParams crop
 #' @param x An SFE object
@@ -25,6 +28,13 @@
 #' @param min_area Minimum area in the same unit as the geometry coordinates
 #'   (squared) for each piece to be considered a separate piece when splitting
 #'   by contiguity. Only pieces that are large enough are considered.
+#' @param colGraphName Name of graph to use for \code{splitComponent}. We
+#' recommend distance based neighbors (`dnearneigh` in 
+#' \code{\link{findSpatialNeighbors}}), and recommend NOT using k nearest
+#' neighbors (`knearneigh`) or triangulation (`tri2nb`).
+#' @param min_cells Minimum number of cells per graph component; components with
+#' fewer than this number of cells are considered debris and removed.
+#' 
 #' @return A list of SFE objects.
 #' @concept Geometric operations
 #' @name splitByCol
@@ -105,4 +115,18 @@ splitContiguity <- function(x, colGeometryName = 1L,
     splitByCol(x, ag_union, colGeometryName = colGeometryName, cover = cover)
 }
 
-# TODO: split by graph components
+#' @importFrom spdep n.comp.nb
+#' @importFrom S4Vectors split
+#' @rdname splitByCol
+#' @export
+splitComponent <- function(x, colGraphName = 1L, min_cells = 100) {
+    g <- colGraph(x, colGraphName)
+    comps <- n.comp.nb(g$neighbours)
+    n_cells <- table(comps$comp.id)
+    sfes <- split(x, comps$comp.id)
+    if (any(n_cells < min_cells)) {
+        inds <- n_cells >= min_cells
+        sfes <- sfes[inds]
+    }
+    sfes
+}

man/spatialGraphs.Rd

@@ -86,4 +86,12 @@ test_that("Split by contiguity of an annotGeometry", {
     # When it has pieces that are too small
 })
 
+test_that("Split by graph component", {
+    colGraph(sfe, "dnn") <- findSptialNeighbors(sfe, method = "dnearneigh", d2 = 25)
+    sfes <- splitComponent(sfe, colGraphName = "dnn")
+    classes <- vapply(sfes, class, FUN.VALUE = character(1))
+    expect_true(all(classes == "SpatialFeatureExperiment"))
+    expect_equal(length(sfes), 2L)
+})
+
 unlink(fn, recursive = TRUE)