prepare for release, fixes laplacian issues with igraph 2.0.0, issue #18

countland-R/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: countland
 Title: Analysis of Biological Count Data, Especially from Single-Cell RNA-Seq
-Version: 0.1.1
+Version: 0.1.2
 Authors@R: 
     person("Church", "Samuel H.", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-8451-103X"))
@@ -26,7 +26,7 @@ Description: A set of functions for applying a
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.0
 URL: https://github.com/shchurch/countland
 BugReports: https://github.com/shchurch/countland/issues
 Imports:

countland-R/NEWS.md

@@ -0,0 +1,8 @@
+# countland 0.1.2
+
+* `ScikitManifoldSpectralEmbedding()`, the spectral embedding utility function, now works with behavior of `igraph` v. 2.0.0, by removing self-loops in the adjacency matrix (setting `diag = F`). In addition the function was changed from the deprecated `igraph::graph.adjacency()` to `igraph::graph_from_adjacency_matrix()` (#18).
+
+# countland 0.1.1
+
+* Added a `NEWS.md` file to track changes to the package.
+

countland-R/R/countland_embed.R

@@ -6,7 +6,7 @@
 #' @return matrix of eigenvectors
 ScikitManifoldSpectralEmbedding <- function(A,n_components){
 	# calculate normalized graph laplacian using igraph
-	Ai <- igraph::as.undirected(igraph::graph.adjacency(A,weighted=T))
+	Ai <- igraph::graph_from_adjacency_matrix(A,mode="undirected",weighted=T,diag=F)
 	L <- igraph::laplacian_matrix(Ai,normalized=T)
 	L <- L * -1 # flip sign to match scikit