git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@117653 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -1,5 +1,7 @@ |
1 | 1 |
CHANGES IN VERSION 1.5.4 |
2 | 2 |
------------------------ |
3 |
+ o use byte compiler <2016-05-18, Wed> |
|
4 |
+ o change any(is.na()) to anyNA() which is more efficient <2016-05-18, Wed> |
|
3 | 5 |
o https://github.com/Bioconductor-mirror/ggtree/commit/559548c66b51253e8ccb983d353385838a81f106 |
4 | 6 |
|
5 | 7 |
CHANGES IN VERSION 1.5.3 |
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@@ -471,7 +471,7 @@ fortify.phylo <- function(model, data, layout="rectangular", |
471 | 471 |
} |
472 | 472 |
|
473 | 473 |
if (! is.null(tree$edge.length)) { |
474 |
- if (any(is.na(tree$edge.length))) { |
|
474 |
+ if (anyNA(tree$edge.length)) { |
|
475 | 475 |
warning("'edge.length' contains NA values...\n## setting 'edge.length' to NULL automatically when plotting the tree...") |
476 | 476 |
tree$edge.length <- NULL |
477 | 477 |
} |
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@@ -16,7 +16,7 @@ reroot_node_mapping <- function(tree, tree2) { |
16 | 16 |
|
17 | 17 |
cc <- getChild(tree, ip) |
18 | 18 |
node2 <- node_map[cc,2] |
19 |
- if (any(is.na(node2))) { |
|
19 |
+ if (anyNA(node2)) { |
|
20 | 20 |
node <- c(node, k) |
21 | 21 |
next |
22 | 22 |
} |
... | ... |
@@ -341,7 +341,7 @@ getXcoord2 <- function(x, root, parent, child, len, start=0, rev=FALSE) { |
341 | 341 |
if (rev == TRUE) { |
342 | 342 |
direction <- -1 |
343 | 343 |
} |
344 |
- while(any(is.na(x))) { |
|
344 |
+ while(anyNA(x)) { |
|
345 | 345 |
idx <- which(parent %in% currentNode) |
346 | 346 |
newNode <- child[idx] |
347 | 347 |
x[newNode] <- x[parent[idx]]+len[idx] * direction |
... | ... |
@@ -369,7 +369,7 @@ getXcoord_no_length <- function(tr) { |
369 | 369 |
child_list <- list() |
370 | 370 |
child_list[as.numeric(names(cl))] <- cl |
371 | 371 |
|
372 |
- while(any(is.na(x))) { |
|
372 |
+ while(anyNA(x)) { |
|
373 | 373 |
idx <- match(currentNode, child) |
374 | 374 |
pNode <- parent[idx] |
375 | 375 |
## child number table |
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@@ -450,7 +450,7 @@ getYcoord <- function(tr, step=1) { |
450 | 450 |
y[-tip.idx] <- NA |
451 | 451 |
|
452 | 452 |
currentNode <- 1:Ntip |
453 |
- while(any(is.na(y))) { |
|
453 |
+ while(anyNA(y)) { |
|
454 | 454 |
pNode <- unique(parent[child %in% currentNode]) |
455 | 455 |
## piping of magrittr is slower than nested function call. |
456 | 456 |
## pipeR is fastest, may consider to use pipeR |
... | ... |
@@ -490,7 +490,7 @@ getYcoord_scale <- function(tr, df, yscale) { |
490 | 490 |
child <- edge[,2] |
491 | 491 |
|
492 | 492 |
currentNodes <- root |
493 |
- while(any(is.na(y))) { |
|
493 |
+ while(anyNA(y)) { |
|
494 | 494 |
newNodes <- c() |
495 | 495 |
for (currentNode in currentNodes) { |
496 | 496 |
idx <- which(parent %in% currentNode) |
... | ... |
@@ -564,7 +564,7 @@ getYcoord_scale2 <- function(tr, df, yscale) { |
564 | 564 |
child <- df[, "node"] |
565 | 565 |
|
566 | 566 |
currentNodes <- root |
567 |
- while(any(is.na(y))) { |
|
567 |
+ while(anyNA(y)) { |
|
568 | 568 |
newNodes <- c() |
569 | 569 |
for (currentNode in currentNodes) { |
570 | 570 |
idx <- which(parent %in% currentNode) |
... | ... |
@@ -594,7 +594,7 @@ getYcoord_scale_numeric <- function(tr, df, yscale, ...) { |
594 | 594 |
|
595 | 595 |
y <- df[, yscale] |
596 | 596 |
|
597 |
- if (any(is.na(y))) { |
|
597 |
+ if (anyNA(y)) { |
|
598 | 598 |
warning("NA found in y scale mapping, all were setting to 0") |
599 | 599 |
y[is.na(y)] <- 0 |
600 | 600 |
} |
... | ... |
@@ -674,7 +674,7 @@ getYcoord_scale_category <- function(tr, df, yscale, yscale_mapping=NULL, ...) { |
674 | 674 |
|
675 | 675 |
y <- df[, yscale] |
676 | 676 |
|
677 |
- if (any(is.na(y))) { |
|
677 |
+ if (anyNA(y)) { |
|
678 | 678 |
warning("NA found in y scale mapping, all were setting to 0") |
679 | 679 |
y[is.na(y)] <- 0 |
680 | 680 |
} |
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@@ -753,7 +753,7 @@ set_branch_length <- function(tree_object, branch.length) { |
753 | 753 |
|
754 | 754 |
|
755 | 755 |
re_assign_ycoord_df <- function(df, currentNode) { |
756 |
- while(any(is.na(df$y))) { |
|
756 |
+ while(anyNA(df$y)) { |
|
757 | 757 |
pNode <- with(df, parent[match(currentNode, node)]) %>% unique |
758 | 758 |
idx <- sapply(pNode, function(i) with(df, all(node[parent == i & parent != node] %in% currentNode))) |
759 | 759 |
newNode <- pNode[idx] |