Merge pull request #110 from kharchenkolab/dev

Version 1.4.3

CHANGELOG.md

@@ -1,5 +1,11 @@
 ## Upcoming
 
+## [1.4.3] - 2021-02-08
+
+### Changed
+- Fix the function `parseCellGroups()`, check if clustering exists
+
+
 ## [1.4.2] - 2021-28-06
 
 ### Changed

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: conos
 Title: Clustering on Network of Samples
-Version: 1.4.2
+Version: 1.4.3
 Authors@R: c(person("Viktor","Petukhov", email="[email protected]", role="aut"), person("Nikolas","Barkas", email="[email protected]", role="aut"), person("Peter", "Kharchenko", email = "[email protected]", role = "aut"), person("Weiliang", "Qiu", email = "[email protected]", role = c("ctb")), person("Evan", "Biederstedt", email="[email protected]", role=c("aut", "cre")))
 Description: Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.
 License: GPL-3

R/conos.R

@@ -1152,6 +1152,7 @@ findSubcommunities <- function(con, target.clusters, clustering=NULL, groups=NUL
 
 #' @keywords internal
 parseCellGroups <- function(con, clustering, groups, parse.clusters=TRUE) {
+
   if (!parse.clusters){
     return(groups)
   }
@@ -1163,15 +1164,18 @@ parseCellGroups <- function(con, clustering, groups, parse.clusters=TRUE) {
     return(groups)
   }
 
+  if (length(con$clusters) < 1){
+    stop("Generate a joint clustering first")
+  } else if (!(clustering %in% names(con$clusters)) && !is.null(clustering)) {
+    stop(paste("Clustering",clustering,"does not exist, run findCommunity() first"))
+  }
+
   if (is.null(clustering)) {
     if (length(con$clusters) > 0){
       return(con$clusters[[1]]$groups)
     }
     stop("Either 'groups' must be provided or the conos object must have some clustering estimated")
   }
-  if (is.null(clusters[[clustering]])){
-    stop(paste("Clustering",clustering,"doesn't exist, run findCommunity() first"))
-  }
 
   return(con$clusters[[clustering]]$groups)
 }