@@ -2,7 +2,7 @@ Package: ggtree

 Type: Package

 Title: an R package for visualization and annotation of phylogenetic trees with

     their covariates and other associated data

-Version: 1.11.4

+Version: 1.11.5

 Authors@R: c(

 	   person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),

 	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com",   role = c("aut", "ths")),

@@ -1,3 +1,8 @@

+# ggtree 1.11.5

+

++ fine tune y position after flip; flip compatible with collapse

+    - <https://groups.google.com/d/msgid/bioc-ggtree/1d06342c-9645-4f71-9e66-7d7a7099bf0b%40googlegroups.com?utm_medium=email&utm_source=footer>

+

 # ggtree 1.11.4

 + re-implement collapse as collapse.ggtree method by importing dplyr::collapse

@@ -215,8 +215,8 @@ flip <- function(tree_view=NULL, node1, node2) {

     sp1.df <- df[sp1,]

     sp2.df <- df[sp2,]

-    min_y1 <- min(sp1.df$y)

-    min_y2 <- min(sp2.df$y)

+    min_y1 <- min(sp1.df$y, na.rm=TRUE)

+    min_y2 <- min(sp2.df$y, na.rm=TRUE)

     if (min_y1 < min_y2) {

         tmp <- sp1.df

@@ -227,16 +227,19 @@ flip <- function(tree_view=NULL, node1, node2) {

         sp2 <- tmp

     }

-    min_y1 <- min(sp1.df$y)

-    min_y2 <- min(sp2.df$y)

+    min_y1 <- min(sp1.df$y, na.rm=TRUE)

+    min_y2 <- min(sp2.df$y, na.rm=TRUE)

-    space <- min(sp1.df$y) - max(sp2.df$y)

+    space <- min(sp1.df$y, na.rm=TRUE) - max(sp2.df$y, na.rm=TRUE)

     sp1.df$y <- sp1.df$y - abs(min_y1 - min_y2)

-    sp2.df$y <- sp2.df$y + max(sp1.df$y) + space - min(sp2.df$y)

+    sp2.df$y <- sp2.df$y + max(sp1.df$y, na.rm=TRUE) + space - min(sp2.df$y, na.rm=TRUE)

     df[sp1, "y"] <- sp1.df$y

     df[sp2, "y"] <- sp2.df$y

+    yy <- df$y[-c(sp1, sp2)]

+    df$y[-c(sp1, sp2)] <- yy + ((min(sp2.df$y, na.rm=TRUE) - max(yy)) - (min(yy) - max(sp1.df$y, na.rm=TRUE)))/2

+

     anc <- getAncestor.df(df, node1)

     ii <- match(anc, df$node)

     df[ii, "y"] <- NA

@@ -1483,7 +1483,8 @@ re_assign_ycoord_df <- function(df, currentNode) {

         idx <- sapply(pNode, function(i) with(df, all(node[parent == i & parent != node] %in% currentNode)))

         newNode <- pNode[idx]

         ## newNode <- newNode[is.na(df[match(newNode, df$node), "y"])]

-

+        if (length(newNode) == 0)

+            break

         df[match(newNode, df$node), "y"] <- sapply(newNode, function(i) {

             with(df, mean(y[parent == i], na.rm = TRUE))

         })