| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: ggtree |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: an R package for visualization of tree and annotation data |
| 4 |
-Version: 3.5.0.900 |
|
| 4 |
+Version: 3.5.0.901 |
|
| 5 | 5 |
Authors@R: c( |
| 6 | 6 |
person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"),
|
| 7 | 7 |
comment = c(ORCID = "0000-0002-6485-8781")), |
| ... | ... |
@@ -25,8 +25,9 @@ |
| 25 | 25 |
|
| 26 | 26 |
--> |
| 27 | 27 |
|
| 28 |
-# ggtree 3.5.0.900 |
|
| 28 |
+# ggtree 3.5.0.901 |
|
| 29 | 29 |
|
| 30 |
++ `update_edge_hclust()` to adjust edge length of a `phylo` object converted from a `hclust` object via `ape::as.phylo()` (2022-06-05, Sun) |
|
| 30 | 31 |
+ new 'slanted' layout for `branch.length = 'none'` (2022-04-29, Fri, #497) |
| 31 | 32 |
- only works for Cartesian coordination, that means it will not work for `layout = 'radial'` |
| 32 | 33 |
|
| ... | ... |
@@ -904,9 +904,7 @@ getYcoord <- function(tr, step=1, tip.order = NULL) {
|
| 904 | 904 |
y[-tip.idx] <- NA |
| 905 | 905 |
|
| 906 | 906 |
|
| 907 |
- ## use lookup table |
|
| 908 |
- pvec <- integer(max(tr$edge)) |
|
| 909 |
- pvec[child] = parent |
|
| 907 |
+ pvec <- edge2vec(tr) |
|
| 910 | 908 |
|
| 911 | 909 |
currentNode <- 1:Ntip |
| 912 | 910 |
while(anyNA(y)) {
|
| ... | ... |
@@ -1308,3 +1306,47 @@ getYcoord_no_length_slanted <- function(y){
|
| 1308 | 1306 |
y <- unname(y[order(as.numeric(names(y)))]) |
| 1309 | 1307 |
return(y) |
| 1310 | 1308 |
} |
| 1309 |
+ |
|
| 1310 |
+ |
|
| 1311 |
+edge2vec <- function(tr) {
|
|
| 1312 |
+ parent <- tr$edge[,1] |
|
| 1313 |
+ child <- tr$edge[,2] |
|
| 1314 |
+ |
|
| 1315 |
+ ## use lookup table |
|
| 1316 |
+ pvec <- integer(max(tr$edge)) |
|
| 1317 |
+ pvec[child] <- parent |
|
| 1318 |
+ return(pvec) |
|
| 1319 |
+} |
|
| 1320 |
+ |
|
| 1321 |
+ |
|
| 1322 |
+extract_inode_hclust_item <- function(h, i, ev) {
|
|
| 1323 |
+ j <- h$merge[i,] |
|
| 1324 |
+ if (any(j < 0)) {
|
|
| 1325 |
+ j2 <- j[j < 0][1] |
|
| 1326 |
+ res <- ev[abs(j2)] |
|
| 1327 |
+ } else {
|
|
| 1328 |
+ res <- ev[extract_inode_hclust_item(h, j, ev)] |
|
| 1329 |
+ } |
|
| 1330 |
+ return(res) |
|
| 1331 |
+} |
|
| 1332 |
+ |
|
| 1333 |
+ |
|
| 1334 |
+ |
|
| 1335 |
+# tr is converted from h via ape::as.phylo |
|
| 1336 |
+update_edge_hclust <- function(tr, h) {
|
|
| 1337 |
+ ev <- edge2vec(tr) |
|
| 1338 |
+ |
|
| 1339 |
+ nodes <- vapply(seq_along(h$height), function(i) {
|
|
| 1340 |
+ extract_inode_hclust_item(h, i, ev) |
|
| 1341 |
+ }, numeric(1)) |
|
| 1342 |
+ |
|
| 1343 |
+ len <- numeric(max(tr$edge)) |
|
| 1344 |
+ len[nodes] <- h$height |
|
| 1345 |
+ pn <- ev[nodes] |
|
| 1346 |
+ pn[pn == 0] <- rootnode(tr) |
|
| 1347 |
+ len[nodes] <- len[pn] - len[nodes] |
|
| 1348 |
+ len[1:Ntip(tr)] <- max(h$height)/10 |
|
| 1349 |
+ |
|
| 1350 |
+ tr$edge.length <- len[tr$edge[,2]] |
|
| 1351 |
+ return(tr) |
|
| 1352 |
+} |
