Update clonalCluster

Fixed issue with clustering naming, adding manual and vignette info for clarification, updated testthat

R/clonalCluster.R

@@ -28,6 +28,7 @@
 #' The higher the number the more similarity of sequence will be 
 #' used for clustering.
 #' @param group.by The column header used for to group contigs.
+#' If (\strong{NULL}), clusters will be calculated across samples.
 #' @param exportGraph Return an igraph object of connected 
 #' sequences (\strong{TRUE}) or the amended input with a
 #' new cluster-based variable (\strong{FALSE}).
@@ -98,14 +99,13 @@ clonalCluster <- function(input.data,
                           group_by(bound[,ref2]) %>%
                           dplyr::summarize(sample_count = n(),
                                     unique_samples = paste0(unique(group.by), collapse = ","))
-    dictionary <- list(bound)
   } else {
     bound <- bind_rows(dat)
     graph.variables <- bind_rows(dat) %>%
                           group_by(bound[,ref2]) %>%
                           dplyr::summarize(sample_count = n())
-    dictionary <- dat
   }
+  dictionary <- dat
   #Generating Connected Component
   output.list <- lapply(dictionary, function(x) {
     cluster <- .lvCompare(x, 

vignettes/articles/Clonal_Cluster.Rmd

@@ -78,7 +78,7 @@ head(sub_combined[,c(1,2,13)])
 
 ### Clustering with a single-cell object
 
-If performed over the number of samples, such as the list elements, **group.by** can used to calculate only the clusters on the setting of patient sample (**group.by** = "Patient") or tissue type (**group.by** = "Type"). This will add the selected group to the beginning of the cluster designation. We can also call ```clonalCluster()``` directly on a Single-Cell Object.
+If performed over the number of samples, such as the list elements, **group.by** can used to calculate only the clusters on the setting of patient sample (**group.by** = "Patient") or tissue type (**group.by** = "Type"). This will add the selected group to the beginning of the cluster designation. We can also call ```clonalCluster()``` directly on a Single-Cell Object. If **group.by** = NULL (**default**), the clusters will be calculated across all samples. 
 
 ```{r tidy = FALSE}
 #Adding patient information