Merge pull request #70 from Cristianetaniguti/main

bugfix
mmollina · Jan 4, 2024 · 055f39c · 055f39c
2 parents 17dc262 + d1f889b
commit 055f39c
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Showing 2 changed files with 1,142 additions and 1,136 deletions.
diff --git a/R/build_map_by_steps.R b/R/build_map_by_steps.R
@@ -197,7 +197,7 @@ update_framework_map <- function(input.map.list,
                               method = "hmm", 
                               verbose = verbose)
 
-    a <- rem_mrk_clusters(cur.res$map, 
+    a <- rem_mrk_clusters(input.map = cur.res$map, 
                           size.rem.cluster = size.rem.cluster, 
                           gap.threshold = gap.threshold)
 
@@ -337,7 +337,7 @@ add_md_markers <- function(input.map,
                            thresh = 500, 
                            extend.tail = 50,
                            method = c("hmm", "wMDS_to_1D_pc"), 
-                           verbose = T){
+                           verbose = TRUE){
   method <- match.arg(method)
   if(method == "wMDS_to_1D_pc" & is.null(input.mds))
     stop("you must provide 'input.mds' when selecting method = 'wMDS_to_1D_pc'", call. = FALSE)
@@ -435,6 +435,7 @@ rem_mrk_clusters <- function(input.map,
   id <- cbind(c(1, id+1), c(id, input.map$info$n.mrk))
   ## Selecting map segments larger then the specified threshold
   segments <- id[apply(id, 1, diff) > size.rem.cluster - 1, , drop = FALSE]
+  if(dim(segments)[1] == 0) stop("All markers were discarted using the defined gap.threshold.")
   id<-NULL
   for(i in 1:nrow(segments)){
     id <- c(id, segments[i,1]:segments[i,2])