... | ... |
@@ -15,19 +15,11 @@ setMethod("groupClade", signature(object="codeml"), |
15 | 15 |
|
16 | 16 |
##' @rdname groupClade-methods |
17 | 17 |
##' @exportMethod groupClade |
18 |
-setMethod("groupClade", signature(object="gg"), |
|
18 |
+setMethod("groupClade", signature(object="ggtree"), |
|
19 | 19 |
function(object, node, group_name) { |
20 |
- groupClade.ggplot(object, node, group_name) |
|
20 |
+ groupClade.ggtree(object, node, group_name) |
|
21 | 21 |
}) |
22 | 22 |
|
23 |
-##' @rdname groupClade-methods |
|
24 |
-##' @exportMethod groupClade |
|
25 |
-setMethod("groupClade", signature(object="ggplot"), |
|
26 |
- function(object, node, group_name) { |
|
27 |
- groupClade.ggplot(object, node, group_name) |
|
28 |
- }) |
|
29 |
- |
|
30 |
- |
|
31 | 23 |
##' @rdname groupClade-methods |
32 | 24 |
##' @exportMethod groupClade |
33 | 25 |
setMethod("groupClade", signature(object="jplace"), |
... | ... |
@@ -38,7 +30,7 @@ setMethod("groupClade", signature(object="jplace"), |
38 | 30 |
|
39 | 31 |
##' group selected clade |
40 | 32 |
##' |
41 |
-##' |
|
33 |
+##' |
|
42 | 34 |
##' @rdname groupClade-methods |
43 | 35 |
##' @exportMethod groupClade |
44 | 36 |
setMethod("groupClade", signature(object="nhx"), |
... | ... |
@@ -73,7 +65,7 @@ groupClade.phylo <- function(object, node, group_name) { |
73 | 65 |
clade$tip.label |
74 | 66 |
}) |
75 | 67 |
} |
76 |
- |
|
68 |
+ |
|
77 | 69 |
groupOTU.phylo(object, tips, group_name) |
78 | 70 |
} |
79 | 71 |
|
... | ... |
@@ -88,7 +80,7 @@ groupClade_ <- function(object, node, group_name) { |
88 | 80 |
} |
89 | 81 |
|
90 | 82 |
|
91 |
-groupClade.ggplot <- function(object, nodes, group_name) { |
|
83 |
+groupClade.ggtree <- function(object, nodes, group_name) { |
|
92 | 84 |
df <- object$data |
93 | 85 |
df[, group_name] <- 0 |
94 | 86 |
for (node in nodes) { |
... | ... |
@@ -32,18 +32,12 @@ setMethod("groupOTU", signature(object="codeml_mlc"), |
32 | 32 |
} |
33 | 33 |
) |
34 | 34 |
|
35 |
-##' @rdname groupOTU-methods |
|
36 |
-##' @exportMethod groupOTU |
|
37 |
-setMethod("groupOTU", signature(object="gg"), |
|
38 |
- function(object, focus, group_name, ...) { |
|
39 |
- groupOTU.ggplot(object, focus, group_name, ...) |
|
40 |
- }) |
|
41 | 35 |
|
42 | 36 |
##' @rdname groupOTU-methods |
43 | 37 |
##' @exportMethod groupOTU |
44 |
-setMethod("groupOTU", signature(object="ggplot"), |
|
38 |
+setMethod("groupOTU", signature(object="ggtree"), |
|
45 | 39 |
function(object, focus, group_name="group", ...) { |
46 |
- groupOTU.ggplot(object, focus, group_name, ...) |
|
40 |
+ groupOTU.ggtree(object, focus, group_name, ...) |
|
47 | 41 |
}) |
48 | 42 |
|
49 | 43 |
|
... | ... |
@@ -185,7 +179,7 @@ groupOTU_ <- function(object, focus, group_name, ...) { |
185 | 179 |
} |
186 | 180 |
|
187 | 181 |
|
188 |
-groupOTU.ggplot <- function(object, focus, group_name, ...) { |
|
182 |
+groupOTU.ggtree <- function(object, focus, group_name, ...) { |
|
189 | 183 |
df <- object$data |
190 | 184 |
df[, group_name] <- 0 |
191 | 185 |
object$data <- groupOTU.df(df, focus, group_name, ...) |
... | ... |
@@ -38,7 +38,7 @@ gzoom.phylo <- function(phy, focus, subtree=FALSE, widths=c(.3, .7)) { |
38 | 38 |
invisible(list(p1=p1, p2=p2)) |
39 | 39 |
} |
40 | 40 |
|
41 |
-gzoom.ggplot <- function(tree_view, focus, widths=c(.3, .7), xmax_adjust=0) { |
|
41 |
+gzoom.ggtree <- function(tree_view, focus, widths=c(.3, .7), xmax_adjust=0) { |
|
42 | 42 |
node <- MRCA(tree_view, focus) |
43 | 43 |
cpos <- get_clade_position(tree_view, node) |
44 | 44 |
p2 <- with(cpos, tree_view+ |
... | ... |
@@ -51,9 +51,9 @@ gzoom.ggplot <- function(tree_view, focus, widths=c(.3, .7), xmax_adjust=0) { |
51 | 51 |
##' @rdname gzoom-methods |
52 | 52 |
##' @exportMethod gzoom |
53 | 53 |
##' @param xmax_adjust adjust xmax (xlim[2]) |
54 |
-setMethod("gzoom", signature(object="gg"), |
|
54 |
+setMethod("gzoom", signature(object="ggtree"), |
|
55 | 55 |
function(object, focus, widths=c(.3, .7), xmax_adjust=0) { |
56 |
- gzoom.ggplot(object, focus, widths, xmax_adjust) |
|
56 |
+ gzoom.ggtree(object, focus, widths, xmax_adjust) |
|
57 | 57 |
}) |
58 | 58 |
|
59 | 59 |
|
60 | 60 |
deleted file mode 100644 |
... | ... |
@@ -1,803 +0,0 @@ |
1 |
-##' convert tip or node label(s) to internal node number |
|
2 |
-##' |
|
3 |
-##' |
|
4 |
-##' @title nodeid |
|
5 |
-##' @param x tree object or graphic object return by ggtree |
|
6 |
-##' @param label tip or node label(s) |
|
7 |
-##' @return internal node number |
|
8 |
-##' @export |
|
9 |
-##' @author Guangchuang Yu |
|
10 |
-nodeid <- function(x, label) { |
|
11 |
- if (is(x, "gg")) |
|
12 |
- return(nodeid.gg(x, label)) |
|
13 |
- |
|
14 |
- nodeid.tree(x, label) |
|
15 |
-} |
|
16 |
- |
|
17 |
-nodeid.tree <- function(tree, label) { |
|
18 |
- tr <- get.tree(tree) |
|
19 |
- lab <- c(tr$tip.label, tr$node.label) |
|
20 |
- match(label, lab) |
|
21 |
-} |
|
22 |
- |
|
23 |
-nodeid.gg <- function(p, label) { |
|
24 |
- p$data$node[match(label, p$data$label)] |
|
25 |
-} |
|
26 |
- |
|
27 |
- |
|
28 |
-reroot_node_mapping <- function(tree, tree2) { |
|
29 |
- root <- getRoot(tree) |
|
30 |
- |
|
31 |
- node_map <- data.frame(from=1:getNodeNum(tree), to=NA, visited=FALSE) |
|
32 |
- node_map[1:Ntip(tree), 2] <- match(tree$tip.label, tree2$tip.label) |
|
33 |
- node_map[1:Ntip(tree), 3] <- TRUE |
|
34 |
- |
|
35 |
- node_map[root, 2] <- root |
|
36 |
- node_map[root, 3] <- TRUE |
|
37 |
- |
|
38 |
- node <- rev(tree$edge[,2]) |
|
39 |
- for (k in node) { |
|
40 |
- ip <- getParent(tree, k) |
|
41 |
- if (node_map[ip, "visited"]) |
|
42 |
- next |
|
43 |
- |
|
44 |
- cc <- getChild(tree, ip) |
|
45 |
- node2 <- node_map[cc,2] |
|
46 |
- if (anyNA(node2)) { |
|
47 |
- node <- c(node, k) |
|
48 |
- next |
|
49 |
- } |
|
50 |
- |
|
51 |
- to <- unique(sapply(node2, getParent, tr=tree2)) |
|
52 |
- to <- to[! to %in% node_map[,2]] |
|
53 |
- node_map[ip, 2] <- to |
|
54 |
- node_map[ip, 3] <- TRUE |
|
55 |
- } |
|
56 |
- node_map <- node_map[, -3] |
|
57 |
- return(node_map) |
|
58 |
-} |
|
59 |
- |
|
60 |
- |
|
61 |
- |
|
62 |
-##' @importFrom ape reorder.phylo |
|
63 |
-layout.unrooted <- function(tree) { |
|
64 |
- N <- getNodeNum(tree) |
|
65 |
- root <- getRoot(tree) |
|
66 |
- |
|
67 |
- df <- as.data.frame.phylo_(tree) |
|
68 |
- df$x <- NA |
|
69 |
- df$y <- NA |
|
70 |
- df$start <- NA |
|
71 |
- df$end <- NA |
|
72 |
- df$angle <- NA |
|
73 |
- df[root, "x"] <- 0 |
|
74 |
- df[root, "y"] <- 0 |
|
75 |
- df[root, "start"] <- 0 |
|
76 |
- df[root, "end"] <- 2 |
|
77 |
- df[root, "angle"] <- 0 |
|
78 |
- |
|
79 |
- nb.sp <- sapply(1:N, function(i) length(get.offspring.tip(tree, i))) |
|
80 |
- |
|
81 |
- nodes <- getNodes_by_postorder(tree) |
|
82 |
- |
|
83 |
- for(curNode in nodes) { |
|
84 |
- curNtip <- nb.sp[curNode] |
|
85 |
- children <- getChild(tree, curNode) |
|
86 |
- |
|
87 |
- start <- df[curNode, "start"] |
|
88 |
- end <- df[curNode, "end"] |
|
89 |
- |
|
90 |
- if (length(children) == 0) { |
|
91 |
- ## is a tip |
|
92 |
- next |
|
93 |
- } |
|
94 |
- |
|
95 |
- for (i in seq_along(children)) { |
|
96 |
- child <- children[i] |
|
97 |
- ntip.child <- nb.sp[child] |
|
98 |
- |
|
99 |
- alpha <- (end - start) * ntip.child/curNtip |
|
100 |
- beta <- start + alpha / 2 |
|
101 |
- |
|
102 |
- length.child <- df[child, "length"] |
|
103 |
- df[child, "x"] <- df[curNode, "x"] + cospi(beta) * length.child |
|
104 |
- df[child, "y"] <- df[curNode, "y"] + sinpi(beta) * length.child |
|
105 |
- df[child, "angle"] <- -90 -180 * beta * sign(beta - 1) |
|
106 |
- df[child, "start"] <- start |
|
107 |
- df[child, "end"] <- start + alpha |
|
108 |
- start <- start + alpha |
|
109 |
- } |
|
110 |
- |
|
111 |
- } |
|
112 |
- |
|
113 |
- return(df) |
|
114 |
-} |
|
115 |
- |
|
116 |
-getParent.df <- function(df, node) { |
|
117 |
- i <- which(df$node == node) |
|
118 |
- res <- df$parent[i] |
|
119 |
- if (res == node) { |
|
120 |
- ## root node |
|
121 |
- return(0) |
|
122 |
- } |
|
123 |
- return(res) |
|
124 |
-} |
|
125 |
- |
|
126 |
-getAncestor.df <- function(df, node) { |
|
127 |
- anc <- getParent.df(df, node) |
|
128 |
- anc <- anc[anc != 0] |
|
129 |
- if (length(anc) == 0) { |
|
130 |
- stop("selected node is root...") |
|
131 |
- } |
|
132 |
- i <- 1 |
|
133 |
- while(i<= length(anc)) { |
|
134 |
- anc <- c(anc, getParent.df(df, anc[i])) |
|
135 |
- anc <- anc[anc != 0] |
|
136 |
- i <- i+1 |
|
137 |
- } |
|
138 |
- return(anc) |
|
139 |
-} |
|
140 |
- |
|
141 |
- |
|
142 |
-getChild.df <- function(df, node) { |
|
143 |
- i <- which(df$parent == node) |
|
144 |
- if (length(i) == 0) { |
|
145 |
- return(0) |
|
146 |
- } |
|
147 |
- res <- df[i, "node"] |
|
148 |
- res <- res[res != node] ## node may root |
|
149 |
- return(res) |
|
150 |
-} |
|
151 |
- |
|
152 |
-get.offspring.df <- function(df, node) { |
|
153 |
- sp <- getChild.df(df, node) |
|
154 |
- sp <- sp[sp != 0] |
|
155 |
- if (length(sp) == 0) { |
|
156 |
- stop("input node is a tip...") |
|
157 |
- } |
|
158 |
- |
|
159 |
- i <- 1 |
|
160 |
- while(i <= length(sp)) { |
|
161 |
- sp <- c(sp, getChild.df(df, sp[i])) |
|
162 |
- sp <- sp[sp != 0] |
|
163 |
- i <- i + 1 |
|
164 |
- } |
|
165 |
- return(sp) |
|
166 |
-} |
|
167 |
- |
|
168 |
- |
|
169 |
-##' extract offspring tips |
|
170 |
-##' |
|
171 |
-##' |
|
172 |
-##' @title get.offspring.tip |
|
173 |
-##' @param tr tree |
|
174 |
-##' @param node node |
|
175 |
-##' @return tip label |
|
176 |
-##' @author ygc |
|
177 |
-##' @importFrom ape extract.clade |
|
178 |
-##' @export |
|
179 |
-get.offspring.tip <- function(tr, node) { |
|
180 |
- if ( ! node %in% tr$edge[,1]) { |
|
181 |
- ## return itself |
|
182 |
- return(tr$tip.label[node]) |
|
183 |
- } |
|
184 |
- clade <- extract.clade(tr, node) |
|
185 |
- clade$tip.label |
|
186 |
-} |
|
187 |
- |
|
188 |
- |
|
189 |
-##' calculate total number of nodes |
|
190 |
-##' |
|
191 |
-##' |
|
192 |
-##' @title getNodeNum |
|
193 |
-##' @param tr phylo object |
|
194 |
-##' @return number |
|
195 |
-##' @author Guangchuang Yu |
|
196 |
-##' @export |
|
197 |
-getNodeNum <- function(tr) { |
|
198 |
- Ntip <- length(tr[["tip.label"]]) |
|
199 |
- Nnode <- tr[["Nnode"]] |
|
200 |
- ## total nodes |
|
201 |
- N <- Ntip + Nnode |
|
202 |
- return(N) |
|
203 |
-} |
|
204 |
- |
|
205 |
-getParent <- function(tr, node) { |
|
206 |
- if ( node == getRoot(tr) ) |
|
207 |
- return(0) |
|
208 |
- edge <- tr[["edge"]] |
|
209 |
- parent <- edge[,1] |
|
210 |
- child <- edge[,2] |
|
211 |
- res <- parent[child == node] |
|
212 |
- if (length(res) == 0) { |
|
213 |
- stop("cannot found parent node...") |
|
214 |
- } |
|
215 |
- if (length(res) > 1) { |
|
216 |
- stop("multiple parent found...") |
|
217 |
- } |
|
218 |
- return(res) |
|
219 |
-} |
|
220 |
- |
|
221 |
-getChild <- function(tr, node) { |
|
222 |
- edge <- tr[["edge"]] |
|
223 |
- res <- edge[edge[,1] == node, 2] |
|
224 |
- ## if (length(res) == 0) { |
|
225 |
- ## ## is a tip |
|
226 |
- ## return(NA) |
|
227 |
- ## } |
|
228 |
- return(res) |
|
229 |
-} |
|
230 |
- |
|
231 |
-getSibling <- function(tr, node) { |
|
232 |
- root <- getRoot(tr) |
|
233 |
- if (node == root) { |
|
234 |
- return(NA) |
|
235 |
- } |
|
236 |
- |
|
237 |
- parent <- getParent(tr, node) |
|
238 |
- child <- getChild(tr, parent) |
|
239 |
- sib <- child[child != node] |
|
240 |
- return(sib) |
|
241 |
-} |
|
242 |
- |
|
243 |
- |
|
244 |
-getAncestor <- function(tr, node) { |
|
245 |
- root <- getRoot(tr) |
|
246 |
- if (node == root) { |
|
247 |
- return(NA) |
|
248 |
- } |
|
249 |
- parent <- getParent(tr, node) |
|
250 |
- res <- parent |
|
251 |
- while(parent != root) { |
|
252 |
- parent <- getParent(tr, parent) |
|
253 |
- res <- c(res, parent) |
|
254 |
- } |
|
255 |
- return(res) |
|
256 |
-} |
|
257 |
- |
|
258 |
-isRoot <- function(tr, node) { |
|
259 |
- getRoot(tr) == node |
|
260 |
-} |
|
261 |
- |
|
262 |
-getNodeName <- function(tr) { |
|
263 |
- if (is.null(tr$node.label)) { |
|
264 |
- n <- length(tr$tip.label) |
|
265 |
- nl <- (n + 1):(2 * n - 2) |
|
266 |
- nl <- as.character(nl) |
|
267 |
- } |
|
268 |
- else { |
|
269 |
- nl <- tr$node.label |
|
270 |
- } |
|
271 |
- nodeName <- c(tr$tip.label, nl) |
|
272 |
- return(nodeName) |
|
273 |
-} |
|
274 |
- |
|
275 |
-##' get the root number |
|
276 |
-##' |
|
277 |
-##' |
|
278 |
-##' @title getRoot |
|
279 |
-##' @param tr phylo object |
|
280 |
-##' @return root number |
|
281 |
-##' @export |
|
282 |
-##' @author Guangchuang Yu |
|
283 |
-getRoot <- function(tr) { |
|
284 |
- edge <- tr[["edge"]] |
|
285 |
- ## 1st col is parent, |
|
286 |
- ## 2nd col is child, |
|
287 |
- if (!is.null(attr(tr, "order")) && attr(tr, "order") == "postorder") |
|
288 |
- return(edge[nrow(edge), 1]) |
|
289 |
- |
|
290 |
- parent <- unique(edge[,1]) |
|
291 |
- child <- unique(edge[,2]) |
|
292 |
- ## the node that has no parent should be the root |
|
293 |
- root <- parent[ ! parent %in% child ] |
|
294 |
- if (length(root) > 1) { |
|
295 |
- stop("multiple roots founded...") |
|
296 |
- } |
|
297 |
- return(root) |
|
298 |
-} |
|
299 |
- |
|
300 |
-get.trunk <- function(tr) { |
|
301 |
- root <- getRoot(tr) |
|
302 |
- path_length <- sapply(1:(root-1), function(x) get.path_length(tr, root, x)) |
|
303 |
- i <- which.max(path_length) |
|
304 |
- return(get.path(tr, root, i)) |
|
305 |
-} |
|
306 |
- |
|
307 |
-##' path from start node to end node |
|
308 |
-##' |
|
309 |
-##' |
|
310 |
-##' @title get.path |
|
311 |
-##' @param phylo phylo object |
|
312 |
-##' @param from start node |
|
313 |
-##' @param to end node |
|
314 |
-##' @return node vectot |
|
315 |
-##' @export |
|
316 |
-##' @author Guangchuang Yu |
|
317 |
-get.path <- function(phylo, from, to) { |
|
318 |
- anc_from <- getAncestor(phylo, from) |
|
319 |
- anc_from <- c(from, anc_from) |
|
320 |
- anc_to <- getAncestor(phylo, to) |
|
321 |
- anc_to <- c(to, anc_to) |
|
322 |
- mrca <- intersect(anc_from, anc_to)[1] |
|
323 |
- |
|
324 |
- i <- which(anc_from == mrca) |
|
325 |
- j <- which(anc_to == mrca) |
|
326 |
- |
|
327 |
- path <- c(anc_from[1:i], rev(anc_to[1:(j-1)])) |
|
328 |
- return(path) |
|
329 |
-} |
|
330 |
- |
|
331 |
-get.path_length <- function(phylo, from, to, weight=NULL) { |
|
332 |
- path <- get.path(phylo, from, to) |
|
333 |
- if (is.null(weight)) { |
|
334 |
- return(length(path)-1) |
|
335 |
- } |
|
336 |
- |
|
337 |
- df <- fortify(phylo) |
|
338 |
- if ( ! (weight %in% colnames(df))) { |
|
339 |
- stop("weight should be one of numerical attributes of the tree...") |
|
340 |
- } |
|
341 |
- |
|
342 |
- res <- 0 |
|
343 |
- |
|
344 |
- get_edge_index <- function(df, from, to) { |
|
345 |
- which((df[,1] == from | df[,2] == from) & |
|
346 |
- (df[,1] == to | df[,2] == to)) |
|
347 |
- } |
|
348 |
- |
|
349 |
- for(i in 1:(length(path)-1)) { |
|
350 |
- ee <- get_edge_index(df, path[i], path[i+1]) |
|
351 |
- res <- res + df[ee, weight] |
|
352 |
- } |
|
353 |
- |
|
354 |
- return(res) |
|
355 |
-} |
|
356 |
- |
|
357 |
-getNodes_by_postorder <- function(tree) { |
|
358 |
- tree <- reorder.phylo(tree, "postorder") |
|
359 |
- unique(rev(as.vector(t(tree$edge[,c(2,1)])))) |
|
360 |
-} |
|
361 |
- |
|
362 |
-getXcoord2 <- function(x, root, parent, child, len, start=0, rev=FALSE) { |
|
363 |
- x[root] <- start |
|
364 |
- x[-root] <- NA ## only root is set to start, by default 0 |
|
365 |
- |
|
366 |
- currentNode <- root |
|
367 |
- direction <- 1 |
|
368 |
- if (rev == TRUE) { |
|
369 |
- direction <- -1 |
|
370 |
- } |
|
371 |
- while(anyNA(x)) { |
|
372 |
- idx <- which(parent %in% currentNode) |
|
373 |
- newNode <- child[idx] |
|
374 |
- x[newNode] <- x[parent[idx]]+len[idx] * direction |
|
375 |
- currentNode <- newNode |
|
376 |
- } |
|
377 |
- |
|
378 |
- return(x) |
|
379 |
-} |
|
380 |
- |
|
381 |
-getXcoord_no_length <- function(tr) { |
|
382 |
- edge <- tr$edge |
|
383 |
- parent <- edge[,1] |
|
384 |
- child <- edge[,2] |
|
385 |
- root <- getRoot(tr) |
|
386 |
- |
|
387 |
- len <- tr$edge.length |
|
388 |
- |
|
389 |
- N <- getNodeNum(tr) |
|
390 |
- x <- numeric(N) |
|
391 |
- ntip <- Ntip(tr) |
|
392 |
- currentNode <- 1:ntip |
|
393 |
- x[-currentNode] <- NA |
|
394 |
- |
|
395 |
- cl <- split(child, parent) |
|
396 |
- child_list <- list() |
|
397 |
- child_list[as.numeric(names(cl))] <- cl |
|
398 |
- |
|
399 |
- while(anyNA(x)) { |
|
400 |
- idx <- match(currentNode, child) |
|
401 |
- pNode <- parent[idx] |
|
402 |
- ## child number table |
|
403 |
- p1 <- table(parent[parent %in% pNode]) |
|
404 |
- p2 <- table(pNode) |
|
405 |
- np <- names(p2) |
|
406 |
- i <- p1[np] == p2 |
|
407 |
- newNode <- as.numeric(np[i]) |
|
408 |
- |
|
409 |
- exclude <- rep(NA, max(child)) |
|
410 |
- for (j in newNode) { |
|
411 |
- x[j] <- min(x[child_list[[j]]]) - 1 |
|
412 |
- exclude[child_list[[j]]] <- child_list[[j]] |
|
413 |
- } |
|
414 |
- exclude <- exclude[!is.na(exclude)] |
|
415 |
- |
|
416 |
- ## currentNode %<>% `[`(!(. %in% exclude)) |
|
417 |
- ## currentNode %<>% c(., newNode) %>% unique |
|
418 |
- currentNode <- currentNode[!currentNode %in% exclude] |
|
419 |
- currentNode <- unique(c(currentNode, newNode)) |
|
420 |
- |
|
421 |
- } |
|
422 |
- x <- x - min(x) |
|
423 |
- return(x) |
|
424 |
-} |
|
425 |
- |
|
426 |
- |
|
427 |
-getXcoord <- function(tr) { |
|
428 |
- edge <- tr$edge |
|
429 |
- parent <- edge[,1] |
|
430 |
- child <- edge[,2] |
|
431 |
- root <- getRoot(tr) |
|
432 |
- |
|
433 |
- len <- tr$edge.length |
|
434 |
- |
|
435 |
- N <- getNodeNum(tr) |
|
436 |
- x <- numeric(N) |
|
437 |
- x <- getXcoord2(x, root, parent, child, len) |
|
438 |
- return(x) |
|
439 |
-} |
|
440 |
- |
|
441 |
-getXYcoord_slanted <- function(tr) { |
|
442 |
- |
|
443 |
- edge <- tr$edge |
|
444 |
- parent <- edge[,1] |
|
445 |
- child <- edge[,2] |
|
446 |
- root <- getRoot(tr) |
|
447 |
- |
|
448 |
- N <- getNodeNum(tr) |
|
449 |
- len <- tr$edge.length |
|
450 |
- y <- getYcoord(tr, step=min(len)/2) |
|
451 |
- |
|
452 |
- len <- sqrt(len^2 - (y[parent]-y[child])^2) |
|
453 |
- x <- numeric(N) |
|
454 |
- x <- getXcoord2(x, root, parent, child, len) |
|
455 |
- res <- data.frame(x=x, y=y) |
|
456 |
- return(res) |
|
457 |
-} |
|
458 |
- |
|
459 |
- |
|
460 |
-## @importFrom magrittr %>% |
|
461 |
-##' @importFrom magrittr equals |
|
462 |
-getYcoord <- function(tr, step=1) { |
|
463 |
- Ntip <- length(tr[["tip.label"]]) |
|
464 |
- N <- getNodeNum(tr) |
|
465 |
- |
|
466 |
- edge <- tr[["edge"]] |
|
467 |
- parent <- edge[,1] |
|
468 |
- child <- edge[,2] |
|
469 |
- |
|
470 |
- cl <- split(child, parent) |
|
471 |
- child_list <- list() |
|
472 |
- child_list[as.numeric(names(cl))] <- cl |
|
473 |
- |
|
474 |
- y <- numeric(N) |
|
475 |
- tip.idx <- child[child <= Ntip] |
|
476 |
- y[tip.idx] <- 1:Ntip * step |
|
477 |
- y[-tip.idx] <- NA |
|
478 |
- |
|
479 |
- currentNode <- 1:Ntip |
|
480 |
- while(anyNA(y)) { |
|
481 |
- pNode <- unique(parent[child %in% currentNode]) |
|
482 |
- ## piping of magrittr is slower than nested function call. |
|
483 |
- ## pipeR is fastest, may consider to use pipeR |
|
484 |
- ## |
|
485 |
- ## child %in% currentNode %>% which %>% parent[.] %>% unique |
|
486 |
- ## idx <- sapply(pNode, function(i) all(child[parent == i] %in% currentNode)) |
|
487 |
- idx <- sapply(pNode, function(i) all(child_list[[i]] %in% currentNode)) |
|
488 |
- newNode <- pNode[idx] |
|
489 |
- |
|
490 |
- y[newNode] <- sapply(newNode, function(i) { |
|
491 |
- mean(y[child_list[[i]]], na.rm=TRUE) |
|
492 |
- ##child[parent == i] %>% y[.] %>% mean(na.rm=TRUE) |
|
493 |
- }) |
|
494 |
- |
|
495 |
- currentNode <- c(currentNode[!currentNode %in% unlist(child_list[newNode])], newNode) |
|
496 |
- ## currentNode <- c(currentNode[!currentNode %in% child[parent %in% newNode]], newNode) |
|
497 |
- ## parent %in% newNode %>% child[.] %>% |
|
498 |
- ## `%in%`(currentNode, .) %>% `!` %>% |
|
499 |
- ## currentNode[.] %>% c(., newNode) |
|
500 |
- } |
|
501 |
- |
|
502 |
- return(y) |
|
503 |
-} |
|
504 |
- |
|
505 |
- |
|
506 |
-getYcoord_scale <- function(tr, df, yscale) { |
|
507 |
- |
|
508 |
- N <- getNodeNum(tr) |
|
509 |
- y <- numeric(N) |
|
510 |
- |
|
511 |
- root <- getRoot(tr) |
|
512 |
- y[root] <- 0 |
|
513 |
- y[-root] <- NA |
|
514 |
- |
|
515 |
- edge <- tr$edge |
|
516 |
- parent <- edge[,1] |
|
517 |
- child <- edge[,2] |
|
518 |
- |
|
519 |
- currentNodes <- root |
|
520 |
- while(anyNA(y)) { |
|
521 |
- newNodes <- c() |
|
522 |
- for (currentNode in currentNodes) { |
|
523 |
- idx <- which(parent %in% currentNode) |
|
524 |
- newNode <- child[idx] |
|
525 |
- direction <- -1 |
|
526 |
- for (i in seq_along(newNode)) { |
|
527 |
- y[newNode[i]] <- y[currentNode] + df[newNode[i], yscale] * direction |
|
528 |
- direction <- -1 * direction |
|
529 |
- } |
|
530 |
- newNodes <- c(newNodes, newNode) |
|
531 |
- } |
|
532 |
- currentNodes <- unique(newNodes) |
|
533 |
- } |
|
534 |
- if (min(y) < 0) { |
|
535 |
- y <- y + abs(min(y)) |
|
536 |
- } |
|
537 |
- return(y) |
|
538 |
-} |
|
539 |
- |
|
540 |
-getYcoord_scale2 <- function(tr, df, yscale) { |
|
541 |
- root <- getRoot(tr) |
|
542 |
- |
|
543 |
- pathLength <- sapply(1:length(tr$tip.label), function(i) { |
|
544 |
- get.path_length(tr, i, root, yscale) |
|
545 |
- }) |
|
546 |
- |
|
547 |
- ordered_tip <- order(pathLength, decreasing = TRUE) |
|
548 |
- ii <- 1 |
|
549 |
- ntip <- length(ordered_tip) |
|
550 |
- while(ii < ntip) { |
|
551 |
- sib <- getSibling(tr, ordered_tip[ii]) |
|
552 |
- if (length(sib) == 0) { |
|
553 |
- ii <- ii + 1 |
|
554 |
- next |
|
555 |
- } |
|
556 |
- jj <- which(ordered_tip %in% sib) |
|
557 |
- if (length(jj) == 0) { |
|
558 |
- ii <- ii + 1 |
|
559 |
- next |
|
560 |
- } |
|
561 |
- sib <- ordered_tip[jj] |
|
562 |
- ordered_tip <- ordered_tip[-jj] |
|
563 |
- nn <- length(sib) |
|
564 |
- if (ii < length(ordered_tip)) { |
|
565 |
- ordered_tip <- c(ordered_tip[1:ii],sib, ordered_tip[(ii+1):length(ordered_tip)]) |
|
566 |
- } else { |
|
567 |
- ordered_tip <- c(ordered_tip[1:ii],sib) |
|
568 |
- } |
|
569 |
- |
|
570 |
- ii <- ii + nn + 1 |
|
571 |
- } |
|
572 |
- |
|
573 |
- |
|
574 |
- long_branch <- getAncestor(tr, ordered_tip[1]) %>% rev |
|
575 |
- long_branch <- c(long_branch, ordered_tip[1]) |
|
576 |
- |
|
577 |
- N <- getNodeNum(tr) |
|
578 |
- y <- numeric(N) |
|
579 |
- |
|
580 |
- y[root] <- 0 |
|
581 |
- y[-root] <- NA |
|
582 |
- |
|
583 |
- ## yy <- df[, yscale] |
|
584 |
- ## yy[is.na(yy)] <- 0 |
|
585 |
- |
|
586 |
- for (i in 2:length(long_branch)) { |
|
587 |
- y[long_branch[i]] <- y[long_branch[i-1]] + df[long_branch[i], yscale] |
|
588 |
- } |
|
589 |
- |
|
590 |
- parent <- df[, "parent"] |
|
591 |
- child <- df[, "node"] |
|
592 |
- |
|
593 |
- currentNodes <- root |
|
594 |
- while(anyNA(y)) { |
|
595 |
- newNodes <- c() |
|
596 |
- for (currentNode in currentNodes) { |
|
597 |
- idx <- which(parent %in% currentNode) |
|
598 |
- newNode <- child[idx] |
|
599 |
- newNode <- c(newNode[! newNode %in% ordered_tip], |
|
600 |
- rev(ordered_tip[ordered_tip %in% newNode])) |
|
601 |
- direction <- -1 |
|
602 |
- for (i in seq_along(newNode)) { |
|
603 |
- if (is.na(y[newNode[i]])) { |
|
604 |
- y[newNode[i]] <- y[currentNode] + df[newNode[i], yscale] * direction |
|
605 |
- direction <- -1 * direction |
|
606 |
- } |
|
607 |
- } |
|
608 |
- newNodes <- c(newNodes, newNode) |
|
609 |
- } |
|
610 |
- currentNodes <- unique(newNodes) |
|
611 |
- } |
|
612 |
- if (min(y) < 0) { |
|
613 |
- y <- y + abs(min(y)) |
|
614 |
- } |
|
615 |
- return(y) |
|
616 |
-} |
|
617 |
- |
|
618 |
-getYcoord_scale_numeric <- function(tr, df, yscale, ...) { |
|
619 |
- df <- .assign_parent_status(tr, df, yscale) |
|
620 |
- df <- .assign_child_status(tr, df, yscale) |
|
621 |
- |
|
622 |
- y <- df[, yscale] |
|
623 |
- |
|
624 |
- if (anyNA(y)) { |
|
625 |
- warning("NA found in y scale mapping, all were setting to 0") |
|
626 |
- y[is.na(y)] <- 0 |
|
627 |
- } |
|
628 |
- |
|
629 |
- return(y) |
|
630 |
-} |
|
631 |
- |
|
632 |
-.assign_parent_status <- function(tr, df, variable) { |
|
633 |
- yy <- df[, variable] |
|
634 |
- na.idx <- which(is.na(yy)) |
|
635 |
- if (length(na.idx) > 0) { |
|
636 |
- tree <- get.tree(tr) |
|
637 |
- nodes <- getNodes_by_postorder(tree) |
|
638 |
- for (curNode in nodes) { |
|
639 |
- children <- getChild(tree, curNode) |
|
640 |
- if (length(children) == 0) { |
|
641 |
- next |
|
642 |
- } |
|
643 |
- idx <- which(is.na(yy[children])) |
|
644 |
- if (length(idx) > 0) { |
|
645 |
- yy[children[idx]] <- yy[curNode] |
|
646 |
- } |
|
647 |
- } |
|
648 |
- } |
|
649 |
- df[, variable] <- yy |
|
650 |
- return(df) |
|
651 |
-} |
|
652 |
- |
|
653 |
-.assign_child_status <- function(tr, df, variable, yscale_mapping=NULL) { |
|
654 |
- yy <- df[, variable] |
|
655 |
- if (!is.null(yscale_mapping)) { |
|
656 |
- yy <- yscale_mapping[yy] |
|
657 |
- } |
|
658 |
- |
|
659 |
- na.idx <- which(is.na(yy)) |
|
660 |
- if (length(na.idx) > 0) { |
|
661 |
- tree <- get.tree(tr) |
|
662 |
- nodes <- rev(getNodes_by_postorder(tree)) |
|
663 |
- for (curNode in nodes) { |
|
664 |
- parent <- getParent(tree, curNode) |
|
665 |
- if (parent == 0) { ## already reach root |
|
666 |
- next |
|
667 |
- } |
|
668 |
- idx <- which(is.na(yy[parent])) |
|
669 |
- if (length(idx) > 0) { |
|
670 |
- child <- getChild(tree, parent) |
|
671 |
- yy[parent[idx]] <- mean(yy[child], na.rm=TRUE) |
|
672 |
- } |
|
673 |
- } |
|
674 |
- } |
|
675 |
- df[, variable] <- yy |
|
676 |
- return(df) |
|
677 |
-} |
|
678 |
- |
|
679 |
- |
|
680 |
-getYcoord_scale_category <- function(tr, df, yscale, yscale_mapping=NULL, ...) { |
|
681 |
- if (is.null(yscale_mapping)) { |
|
682 |
- stop("yscale is category variable, user should provide yscale_mapping, |
|
683 |
- which is a named vector, to convert yscale to numberical values...") |
|
684 |
- } |
|
685 |
- if (! is(yscale_mapping, "numeric") || |
|
686 |
- is.null(names(yscale_mapping))) { |
|
687 |
- stop("yscale_mapping should be a named numeric vector...") |
|
688 |
- } |
|
689 |
- |
|
690 |
- if (yscale == "label") { |
|
691 |
- yy <- df[, yscale] |
|
692 |
- ii <- which(is.na(yy)) |
|
693 |
- if (length(ii)) { |
|
694 |
- df[ii, yscale] <- df[ii, "node"] |
|
695 |
- } |
|
696 |
- } |
|
697 |
- |
|
698 |
- ## assign to parent status is more prefer... |
|
699 |
- df <- .assign_parent_status(tr, df, yscale) |
|
700 |
- df <- .assign_child_status(tr, df, yscale, yscale_mapping) |
|
701 |
- |
|
702 |
- y <- df[, yscale] |
|
703 |
- |
|
704 |
- if (anyNA(y)) { |
|
705 |
- warning("NA found in y scale mapping, all were setting to 0") |
|
706 |
- y[is.na(y)] <- 0 |
|
707 |
- } |
|
708 |
- return(y) |
|
709 |
-} |
|
710 |
- |
|
711 |
- |
|
712 |
-add_angle_slanted <- function(res) { |
|
713 |
- dy <- (res[, "y"] - res[res$parent, "y"]) / diff(range(res[, "y"])) |
|
714 |
- dx <- (res[, "x"] - res[res$parent, "x"]) / diff(range(res[, "x"])) |
|
715 |
- theta <- atan(dy/dx) |
|
716 |
- theta[is.na(theta)] <- 0 ## root node |
|
717 |
- res$angle <- theta/pi * 180 |
|
718 |
- branch.y <- (res[res$parent, "y"] + res[, "y"])/2 |
|
719 |
- idx <- is.na(branch.y) |
|
720 |
- branch.y[idx] <- res[idx, "y"] |
|
721 |
- res[, "branch.y"] <- branch.y |
|
722 |
- return(res) |
|
723 |
-} |
|
724 |
- |
|
725 |
-calculate_branch_mid <- function(res) { |
|
726 |
- res$branch <- (res[res$parent, "x"] + res[, "x"])/2 |
|
727 |
- if (!is.null(res$length)) { |
|
728 |
- res$length[is.na(res$length)] <- 0 |
|
729 |
- } |
|
730 |
- res$branch[is.na(res$branch)] <- 0 |
|
731 |
- return(res) |
|
732 |
-} |
|
733 |
- |
|
734 |
- |
|
735 |
-set_branch_length <- function(tree_object, branch.length) { |
|
736 |
- if (is(tree_object, "phylo4d")) { |
|
737 |
- phylo <- as.phylo.phylo4(tree_object) |
|
738 |
- d <- tree_object@data |
|
739 |
- tree_anno <- data.frame(node=rownames(d), d) |
|
740 |
- } else { |
|
741 |
- phylo <- get.tree(tree_object) |
|
742 |
- } |
|
743 |
- |
|
744 |
- if (branch.length %in% c("branch.length", "none")) { |
|
745 |
- return(phylo) |
|
746 |
- } |
|
747 |
- |
|
748 |
- ## if (is(tree_object, "codeml")) { |
|
749 |
- ## tree_anno <- tree_object@mlc@dNdS |
|
750 |
- ## } else |
|
751 |
- |
|
752 |
- if (is(tree_object, "codeml_mlc")) { |
|
753 |
- tree_anno <- tree_object@dNdS |
|
754 |
- } else if (is(tree_object, "beast")) { |
|
755 |
- tree_anno <- tree_object@stats |
|
756 |
- } |
|
757 |
- |
|
758 |
- if (has.extraInfo(tree_object)) { |
|
759 |
- tree_anno <- merge(tree_anno, tree_object@extraInfo, by.x="node", by.y="node") |
|
760 |
- } |
|
761 |
- cn <- colnames(tree_anno) |
|
762 |
- cn <- cn[!cn %in% c('node', 'parent')] |
|
763 |
- |
|
764 |
- length <- match.arg(branch.length, cn) |
|
765 |
- |
|
766 |
- if (all(is.na(as.numeric(tree_anno[, length])))) { |
|
767 |
- stop("branch.length should be numerical attributes...") |
|
768 |
- } |
|
769 |
- |
|
770 |
- edge <- as.data.frame(phylo$edge) |
|
771 |
- colnames(edge) <- c("parent", "node") |
|
772 |
- |
|
773 |
- dd <- merge(edge, tree_anno, |
|
774 |
- by.x = "node", |
|
775 |
- by.y = "node", |
|
776 |
- all.x = TRUE) |
|
777 |
- dd <- dd[match(edge$node, dd$node),] |
|
778 |
- len <- unlist(dd[, length]) |
|
779 |
- len <- as.numeric(len) |
|
780 |
- len[is.na(len)] <- 0 |
|
781 |
- |
|
782 |
- phylo$edge.length <- len |
|
783 |
- |
|
784 |
- return(phylo) |
|
785 |
-} |
|
786 |
- |
|
787 |
- |
|
788 |
-re_assign_ycoord_df <- function(df, currentNode) { |
|
789 |
- while(anyNA(df$y)) { |
|
790 |
- pNode <- with(df, parent[match(currentNode, node)]) %>% unique |
|
791 |
- idx <- sapply(pNode, function(i) with(df, all(node[parent == i & parent != node] %in% currentNode))) |
|
792 |
- newNode <- pNode[idx] |
|
793 |
- ## newNode <- newNode[is.na(df[match(newNode, df$node), "y"])] |
|
794 |
- |
|
795 |
- df[match(newNode, df$node), "y"] <- sapply(newNode, function(i) { |
|
796 |
- with(df, mean(y[parent == i], na.rm = TRUE)) |
|
797 |
- }) |
|
798 |
- traced_node <- as.vector(sapply(newNode, function(i) with(df, node[parent == i]))) |
|
799 |
- currentNode <- c(currentNode[! currentNode %in% traced_node], newNode) |
|
800 |
- } |
|
801 |
- return(df) |
|
802 |
-} |
|
803 |
- |
... | ... |
@@ -1,5 +1,5 @@ |
1 | 1 |
% Generated by roxygen2: do not edit by hand |
2 |
-% Please edit documentation in R/AllGenerics.R, R/NHX.R, R/RAxML.R, R/ape.R, R/beast.R, R/codeml.R, R/codeml_mlc.R, R/hyphy.R, R/jplace.R, R/paml_rst.R, R/phangorn.R, R/r8s.R |
|
2 |
+% Please edit documentation in R/AllGenerics.R, R/RAxML.R, R/ape.R, R/beast.R, R/codeml.R, R/codeml_mlc.R, R/hyphy.R, R/jplace.R, R/paml_rst.R, R/phangorn.R, R/r8s.R, R/treeio.R |
|
3 | 3 |
\docType{methods} |
4 | 4 |
\name{get.fields} |
5 | 5 |
\alias{get.fields} |
... | ... |
@@ -18,8 +18,6 @@ |
18 | 18 |
\usage{ |
19 | 19 |
get.fields(object, ...) |
20 | 20 |
|
21 |
-\S4method{get.fields}{nhx}(object, ...) |
|
22 |
- |
|
23 | 21 |
\S4method{get.fields}{raxml}(object, ...) |
24 | 22 |
|
25 | 23 |
\S4method{get.fields}{apeBootstrap}(object, ...) |
... | ... |
@@ -39,6 +37,8 @@ get.fields(object, ...) |
39 | 37 |
\S4method{get.fields}{phangorn}(object, ...) |
40 | 38 |
|
41 | 39 |
\S4method{get.fields}{r8s}(object, ...) |
40 |
+ |
|
41 |
+\S4method{get.fields}{nhx}(object, ...) |
|
42 | 42 |
} |
43 | 43 |
\arguments{ |
44 | 44 |
\item{object}{one of \code{jplace}, \code{beast}, \code{hyphy}, \code{codeml}, \code{codeml_mlc}, \code{paml_rst} object} |
... | ... |
@@ -7,8 +7,7 @@ |
7 | 7 |
\alias{groupClade,beast-method} |
8 | 8 |
\alias{groupClade,codeml-method} |
9 | 9 |
\alias{groupClade,codeml_mlc-method} |
10 |
-\alias{groupClade,gg-method} |
|
11 |
-\alias{groupClade,ggplot-method} |
|
10 |
+\alias{groupClade,ggtree-method} |
|
12 | 11 |
\alias{groupClade,hyphy-method} |
13 | 12 |
\alias{groupClade,jplace-method} |
14 | 13 |
\alias{groupClade,nhx-method} |
... | ... |
@@ -34,9 +33,7 @@ groupClade(object, node, group_name = "group", ...) |
34 | 33 |
|
35 | 34 |
\S4method{groupClade}{codeml}(object, node, group_name = "group") |
36 | 35 |
|
37 |
-\S4method{groupClade}{gg}(object, node, group_name) |
|
38 |
- |
|
39 |
-\S4method{groupClade}{ggplot}(object, node, group_name) |
|
36 |
+\S4method{groupClade}{ggtree}(object, node, group_name) |
|
40 | 37 |
|
41 | 38 |
\S4method{groupClade}{jplace}(object, node, group_name = "group") |
42 | 39 |
|
... | ... |
@@ -7,8 +7,7 @@ |
7 | 7 |
\alias{groupOTU,beast-method} |
8 | 8 |
\alias{groupOTU,codeml-method} |
9 | 9 |
\alias{groupOTU,codeml_mlc-method} |
10 |
-\alias{groupOTU,gg-method} |
|
11 |
-\alias{groupOTU,ggplot-method} |
|
10 |
+\alias{groupOTU,ggtree-method} |
|
12 | 11 |
\alias{groupOTU,hyphy-method} |
13 | 12 |
\alias{groupOTU,jplace-method} |
14 | 13 |
\alias{groupOTU,nhx-method} |
... | ... |
@@ -34,9 +33,7 @@ groupOTU(object, focus, group_name = "group", ...) |
34 | 33 |
|
35 | 34 |
\S4method{groupOTU}{codeml_mlc}(object, focus, group_name = "group", ...) |
36 | 35 |
|
37 |
-\S4method{groupOTU}{gg}(object, focus, group_name = "group", ...) |
|
38 |
- |
|
39 |
-\S4method{groupOTU}{ggplot}(object, focus, group_name = "group", ...) |
|
36 |
+\S4method{groupOTU}{ggtree}(object, focus, group_name = "group", ...) |
|
40 | 37 |
|
41 | 38 |
\S4method{groupOTU}{jplace}(object, focus, group_name = "group", ...) |
42 | 39 |
|
... | ... |
@@ -7,7 +7,7 @@ |
7 | 7 |
\alias{gzoom,beast-method} |
8 | 8 |
\alias{gzoom,codeml-method} |
9 | 9 |
\alias{gzoom,codeml_mlc-method} |
10 |
-\alias{gzoom,gg-method} |
|
10 |
+\alias{gzoom,ggtree-method} |
|
11 | 11 |
\alias{gzoom,hyphy-method} |
12 | 12 |
\alias{gzoom,nhx-method} |
13 | 13 |
\alias{gzoom,paml_rst-method} |
... | ... |
@@ -28,7 +28,8 @@ gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...) |
28 | 28 |
\S4method{gzoom}{hyphy}(object, focus, subtree = FALSE, widths = c(0.3, |
29 | 29 |
0.7)) |
30 | 30 |
|
31 |
-\S4method{gzoom}{gg}(object, focus, widths = c(0.3, 0.7), xmax_adjust = 0) |
|
31 |
+\S4method{gzoom}{ggtree}(object, focus, widths = c(0.3, 0.7), |
|
32 |
+ xmax_adjust = 0) |
|
32 | 33 |
|
33 | 34 |
\S4method{gzoom}{apeBootstrap}(object, focus, subtree = FALSE, |
34 | 35 |
widths = c(0.3, 0.7)) |