Merge pull request #99 from HelenaLC/nodefix

+`plotCoordGraph`

Author: HelenaLC

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SpatialData
 Title: Representation of Python's SpatialData in R
 Depends: R (>= 4.4)
-Version: 0.99.18
+Version: 0.99.19
 Description: Interface to Python's 'SpatialData', currently including:
     reticulate-based use of 'spatialdata-io' for reading of manufracturer
     data and writing to .zarr, on-disk representation of images/labels as
@@ -38,34 +38,35 @@ Authors@R: c(
 Imports:
     arrow,
     basilisk,
+    BiocFileCache,
+    BiocGenerics,
     dplyr,
     DelayedArray,
     geoarrow,
     graph,
     jsonlite,
+    methods,
+    Rarr,
     RBGL,
+    reticulate,
+    Rgraphviz,
     rlang,
     sf,
+    S4Arrays,
     S4Vectors,
     SingleCellExperiment,
     SummarizedExperiment,
-    zellkonverter,
-    BiocGenerics,
-    S4Arrays,
-    Rarr,
-    reticulate,
-    BiocFileCache,
-    methods
+    zellkonverter
 Suggests:
     anndataR,
     BiocStyle,
     ggnewscale,
     knitr,
+    magick,
+    paws,
     pizzarr,
     Rgraphviz,
-    testthat,
-    magick,
-    paws
+    testthat
 Remotes:
     keller-mark/pizzarr,
     keller-mark/anndataR@spatialdata

NAMESPACE

@@ -20,6 +20,7 @@ export(do_tx_to_ext)
 export(mask)
 export(merfish_demo_path)
 export(path_to_10x_xen_demo)
+export(plotCoordGraph)
 export(readImage)
 export(readLabel)
 export(readPoint)
@@ -95,6 +96,8 @@ importFrom(BiocGenerics,colnames)
 importFrom(BiocGenerics,rownames)
 importFrom(RBGL,sp.between)
 importFrom(Rarr,ZarrArray)
+importFrom(Rgraphviz,layoutGraph)
+importFrom(Rgraphviz,renderGraph)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,coolcat)
 importFrom(S4Vectors,isSequence)
@@ -121,9 +124,11 @@ importFrom(graph,"edgeData<-")
 importFrom(graph,"edgeDataDefaults<-")
 importFrom(graph,"nodeData<-")
 importFrom(graph,"nodeDataDefaults<-")
+importFrom(graph,"nodes<-")
 importFrom(graph,addEdge)
 importFrom(graph,addNode)
 importFrom(graph,edgeData)
+importFrom(graph,graph.par)
 importFrom(graph,graphAM)
 importFrom(graph,nodeData)
 importFrom(graph,nodes)

R/coord_utils.R

@@ -24,7 +24,7 @@
 #' 
 #' # object-wide
 #' g <- CTgraph(x)
-#' graphics.off(); graph::plot(g)
+#' plotCoordGraph(g)
 #' 
 #' # retrieve transformation from element to target space
 #' CTpath(x, "blobs_labels", "sequence")
@@ -349,3 +349,48 @@ setMethod("addCT", "Zattrs", \(x, name, type="identity", data=NULL) {
 #' #' @importFrom EBImage resize
 #' setMethod("translation", "ImageArray", \(x, t, ...) {})
 #' setMethod("transform", "ImageArray", \(x, t) get(t$type)(x, unlist(t[[t$type]])))
+
+# plotCoordGraph() ----
+
+#' @name plotCoordGraph
+#' @title CT graph viz.
+#' @description
+#' given a \code{graphNEL} instance, nodes with \code{nchar>max} are
+#' split and hyphenated at character position \code{floor(nchar/fac)}.
+#' 
+#' @examples
+#' x <- file.path("extdata", "blobs.zarr")
+#' x <- system.file(x, package="SpatialData")
+#' x <- readSpatialData(x, tables=FALSE)
+#' 
+#' g <- CTgraph(x)
+#' plotCoordGraph(g, cex=0.6)
+#' 
+#' @importFrom graph nodes nodes<- graph.par
+#' @importFrom Rgraphviz layoutGraph renderGraph
+#' @export
+plotCoordGraph <- \(g, cex=0.6) {
+    g <- CTgraph(x)
+    g2view <- g # leave 'g' alone
+    nodes(g2view) <- .nodefix(nodes(g2view))
+    graph.par(list(nodes=list(shape="plaintext", cex=cex)))
+    g2view <- layoutGraph(g2view)
+    renderGraph(g2view)
+}
+
+.nodefix <- \(x, fac=2, max=10) {
+    if (any((nc <- nchar(x)) > max))
+        x[nc > max] <- .fixup(x[nc > max], fac)
+    x
+}
+
+.fixup <- \(x, fac) {
+    nc <- nchar(x)
+    hm <- floor(nc/fac)
+    xs <- strsplit(x, "")
+    xu <- lapply(seq_along(xs), \(i) c(
+        xs[[i]][seq_len(hm[i])], "-\n", 
+        xs[[i]][-seq_len(hm[i])]))
+    xu <- lapply(xu, \(z) paste(z, collapse=""))
+    unlist(xu)
+}

inst/NEWS

@@ -1,3 +1,11 @@
+changes in version 0.99.19
+
+- adding code to improve visualization of transformation network (PR #98) 
+
+changes in version 0.99.18
+
+- split off 'SpatialData.plot'
+
 changes in version 0.99.17
 
 - rewrite of points and labels plotting, including 

man/coord-utils.Rd

@@ -136,7 +136,7 @@ We can represent these are a graph as follows:
 
 ```{r cs-graph}
 (g <- CTgraph(x))
-graph::plot(g)
+plotCoordGraph(g)
 ```
 
 The above representation greatly facilitates queries of the transformation(s)