scClustViz is really for beta release as an R package.

DESCRIPTION

@@ -1,9 +1,10 @@
 Package: scClustViz
 Type: Package
 Title: Differential Expression-based scRNAseq Cluster Assessment and Viewing
-Version: 0.1.0
-Authors@R: c(as.person("Brendan T Innes <[email protected]> [aut,cre]"),
-             as.person("Gary D Bader [aut,ths]"))
+Version: 0.2.0
+Date: 2018-08-16
+Authors@R: c(as.person("Brendan T. Innes <[email protected]> [aut,cre]"),
+             as.person("Gary D. Bader [aut,ths]"))
 Description: An interactive R Shiny tool for visualizing single-cell RNAseq clustering 
     results from the Seurat R package or any other analysis pipeline. Its main goal is 
     two-fold: A: to help select a biologically appropriate resolution or K from clustering

R/deTest.R

@@ -68,7 +68,7 @@
 #'       file="for_scClustViz.RData")
 #'  # Save these objects so you'll never have to run this slow function again!
 #'  
-#'  runShiny(filePath="for_scClustViz.RData",annotationDB=org.Mm.eg.db)
+#'  runShiny(filePath="for_scClustViz.RData")
 #' }
 #' 
 #' @seealso \code{\link{readFromSeurat}} or \code{\link{readFromManual}} for reading in 
@@ -83,6 +83,8 @@
 clusterWiseDEtest <- function(il,testAll=TRUE,
                               exponent=2,pseudocount=1,FDRthresh=0.01,
                               threshType="dDR",dDRthresh=0.15,logGERthresh=1) {
+  temp_warn <- options("warn")
+  options(warn=-1)
 
   out <- list(CGS=list(),deTissue=list(),deVS=list(),
               deMarker=list(),deDist=list(),deNeighb=list())
@@ -204,8 +206,6 @@ clusterWiseDEtest <- function(il,testAll=TRUE,
       if (min(sapply(out[["deNeighb"]][[res]],nrow)) < 1) { break }
     }
   }
+  options(warn=temp_warn$warn)
   return(out)
 }
-
-#### removing cluster solutions not tested above. ####
-# il[["cl"]] <- il[["cl"]][names(out[["deNeighb"]])] 

R/importData.R

@@ -39,11 +39,20 @@
 #'       specify the desired cell embeddings.} 
 #'   }
 #'
-#' @examples
+#' @examples 
 #' \dontrun{
-#'  data_for_scClustViz <- readFromSeurat(your_seurat_object)
-#'  rm(your_seurat_object)
+#'  data_for_scClustViz <- readFromSeurat(your_seurat_object,
+#'                                        convertGeneIDs=F)
+#'  rm(your_seurat_object) 
 #'  # All the data scClustViz needs is in 'data_for_scClustViz'.
+#'  
+#'  DE_for_scClustViz <- clusterWiseDEtest(data_for_scClustViz)
+#'  
+#'  save(data_for_scClustViz,DE_for_scClustViz,
+#'       file="for_scClustViz.RData")
+#'  # Save these objects so you'll never have to run this slow function again!
+#'  
+#'  runShiny(filePath="for_scClustViz.RData")
 #' }
 #'
 #' @family importData functions