@@ -1,5 +1,6 @@

 CHANGES IN VERSION 1.1.17

 ------------------------

+ o bug fixed in rm.singleton.newick by adding support of scientific notation in branch length <2015-08-27, Thu>

  o bug fixed in gheatmap, remove inherit aes from ggtree <2015-08-27, Thu>

  o add 'width' parameter to add_legend, now user can specify the width of legend bar <2015-08-27, Thu>

  o add 'colnames_position' parameter to gheatmap, now colnames can be display on the top of heatmap <2015-08-27, Thu> 

@@ -57,9 +57,9 @@ rm.singleton.newick <- function(nwk, outfile = NULL) {

     tree <- readLines(nwk)

     ## remove singleton of tips

-    nodePattern <- "\\w+:[\\.0-9]+"

-    singletonPattern.with.nodename <- paste0(".*(\\(", nodePattern, "\\)\\w+:[\\.0-9]+).*")

-    singletonPattern.wo.nodename <- paste0(".*(\\(", nodePattern, "\\)[\\.0-9]+).*")

+    nodePattern <- "\\w+:[\\.0-9Ee\\+\\-]+"

+    singletonPattern.with.nodename <- paste0(".*(\\(", nodePattern, "\\)\\w+:[\\.0-9Ee\\+\\-]+).*")

+    singletonPattern.wo.nodename <- paste0(".*(\\(", nodePattern, "\\)[\\.0-9Ee\\+\\-]+).*")

     while(length(grep("\\([^,]+\\)", tree)) > 0) {

         singleton <- gsub(singletonPattern.with.nodename, "\\1", tree)

@@ -72,8 +72,8 @@ rm.singleton.newick <- function(nwk, outfile = NULL) {

         tip <- gsub("\\((\\w+).*", "\\1", singleton)

-        len1 <- gsub(".*[^\\.0-9]+([\\.0-9]+)", "\\1", singleton)

-        len2 <- gsub(".*:([.0-9]+)\\).*", "\\1", singleton)

+        len1 <- gsub(".*[^\\.0-9Ee\\+\\-]+([\\.0-9Ee\\+\\-]+)", "\\1", singleton)

+        len2 <- gsub(".*:([\\.0-9Ee\\+\\-]+)\\).*", "\\1", singleton)

         len <- as.numeric(len1) + as.numeric(len2)

         tree <- gsub(singleton, paste0(tip, ":", len), tree, fixed = TRUE)