| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.9.1 |
| 2 | 2 |
------------------------ |
| 3 |
+ o now mapping parameter will passed to segment layer in geom_tiplab(align=T) <2017-06-19, Mon> |
|
| 3 | 4 |
o geom_cladelabel support `angle="auto"` for circular layout tree <2017-05-05, Fri> |
| 4 | 5 |
|
| 5 | 6 |
CHANGES IN VERSION 1.8.0 |
| 6 | 7 |
deleted file mode 100644 |
| ... | ... |
@@ -1,281 +0,0 @@ |
| 1 |
- |
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| 2 |
-## ##' read beast output |
|
| 3 |
-## ##' |
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| 4 |
-## ##' |
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| 5 |
-## ##' @title read.beast |
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| 6 |
-## ##' @param file beast file |
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| 7 |
-## ##' @return \code{beast} object
|
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| 8 |
-## ##' @importFrom ape read.nexus |
|
| 9 |
-## ##' @export |
|
| 10 |
-## ##' @author Guangchuang Yu \url{http://ygc.name}
|
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| 11 |
-## ##' @examples |
|
| 12 |
-## ##' file <- system.file("extdata/BEAST", "beast_mcc.tree", package="ggtree")
|
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| 13 |
-## ##' read.beast(file) |
|
| 14 |
-## read.beast <- function(file) {
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| 15 |
-## translation <- read.trans_beast(file) |
|
| 16 |
-## treetext <- read.treetext_beast(file) |
|
| 17 |
-## stats <- read.stats_beast(file) |
|
| 18 |
-## phylo <- read.nexus(file) |
|
| 19 |
- |
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| 20 |
-## if (length(treetext) == 1) {
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| 21 |
-## obj <- BEAST(file, treetext, translation, stats, phylo) |
|
| 22 |
-## } else {
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| 23 |
-## obj <- lapply(seq_along(treetext), function(i) {
|
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| 24 |
-## BEAST(file, treetext[i], translation, stats[[i]], phylo[[i]]) |
|
| 25 |
-## }) |
|
| 26 |
-## class(obj) <- "beastList" |
|
| 27 |
-## } |
|
| 28 |
-## return(obj) |
|
| 29 |
-## } |
|
| 30 |
- |
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| 31 |
- |
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| 32 |
-## BEAST <- function(file, treetext, translation, stats, phylo) {
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| 33 |
-## stats$node %<>% gsub("\"*'*", "", .)
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| 34 |
- |
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| 35 |
-## fields <- sub("_lower|_upper", "", names(stats)) %>% unique
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| 36 |
-## fields %<>% `[`(.!="node") |
|
| 37 |
- |
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| 38 |
-## phylo <- remove_quote_in_tree_label(phylo) |
|
| 39 |
- |
|
| 40 |
-## obj <- new("beast",
|
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| 41 |
-## fields = fields, |
|
| 42 |
-## treetext = treetext, |
|
| 43 |
-## phylo = phylo, |
|
| 44 |
-## translation = translation, |
|
| 45 |
-## stats = stats, |
|
| 46 |
-## file = filename(file) |
|
| 47 |
-## ) |
|
| 48 |
-## return(obj) |
|
| 49 |
-## } |
|
| 50 |
- |
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| 51 |
-## remove_quote_in_tree_label <- function(phylo) {
|
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| 52 |
-## if (!is.null(phylo$node.label)) {
|
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| 53 |
-## phylo$node.label %<>% gsub("\"*'*", "", .)
|
|
| 54 |
-## } |
|
| 55 |
-## if ( !is.null(phylo$tip.label)) {
|
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| 56 |
-## phylo$tip.label %<>% gsub("\"*'*", "", .)
|
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| 57 |
-## } |
|
| 58 |
-## return(phylo) |
|
| 59 |
-## } |
|
| 60 |
- |
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| 61 |
- |
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| 62 |
-## ##' @rdname get.fields-methods |
|
| 63 |
-## ##' @exportMethod get.fields |
|
| 64 |
-## setMethod("get.fields", signature(object="beast"),
|
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| 65 |
-## function(object, ...) {
|
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| 66 |
-## get.fields.tree(object) |
|
| 67 |
-## } |
|
| 68 |
-## ) |
|
| 69 |
- |
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| 70 |
- |
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| 71 |
-## read.treetext_beast <- function(file) {
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| 72 |
-## beast <- readLines(file) |
|
| 73 |
- |
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| 74 |
-## ii <- grep("[Bb]egin trees;", beast)
|
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| 75 |
-## jj <- grep("[Ee]nd;", beast)
|
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| 76 |
-## jj <- jj[jj > max(ii)][1] |
|
| 77 |
-## jj <- c(ii[-1], jj) |
|
| 78 |
- |
|
| 79 |
-## trees <- sapply(seq_along(ii), function(i) {
|
|
| 80 |
-## tree <- beast[(ii[i]+1):(jj[i]-1)] |
|
| 81 |
-## tree <- tree[grep("\\s*[Tt]ree", tree)]
|
|
| 82 |
-## ## if (length(tree) > 1) {
|
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| 83 |
-## ## tree <- paste0(tree, collapse='') |
|
| 84 |
-## ## } |
|
| 85 |
-## sub("[^(]*", "", tree)
|
|
| 86 |
-## }) |
|
| 87 |
- |
|
| 88 |
-## return(trees) |
|
| 89 |
-## } |
|
| 90 |
- |
|
| 91 |
-## read.trans_beast <- function(file) {
|
|
| 92 |
-## beast <- readLines(file) |
|
| 93 |
-## i <- grep("TRANSLATE", beast, ignore.case = TRUE)
|
|
| 94 |
-## if (length(i) == 0) {
|
|
| 95 |
-## return(matrix()) |
|
| 96 |
-## } |
|
| 97 |
-## end <- grep(";", beast)
|
|
| 98 |
-## j <- end[end %>% `>`(i) %>% which %>% `[`(1)] |
|
| 99 |
-## trans <- beast[(i+1):j] |
|
| 100 |
-## trans %<>% gsub("\\t+", "", .)
|
|
| 101 |
-## trans %<>% gsub(",|;", "", .)
|
|
| 102 |
-## trans %<>% `[`(nzchar(trans)) |
|
| 103 |
-## ## remove quote if strings were quoted |
|
| 104 |
-## trans %<>% gsub("'|\"", "",.)
|
|
| 105 |
-## trans %<>% sapply(., strsplit, split="\\s+") |
|
| 106 |
-## trans %<>% do.call(rbind, .) |
|
| 107 |
-## ## trans is a matrix |
|
| 108 |
-## return(trans) |
|
| 109 |
-## } |
|
| 110 |
- |
|
| 111 |
- |
|
| 112 |
-## read.stats_beast <- function(file) {
|
|
| 113 |
-## beast <- readLines(file) |
|
| 114 |
-## trees <- read.treetext_beast(file) |
|
| 115 |
-## if (length(trees) == 1) {
|
|
| 116 |
-## return(read.stats_beast_internal(beast, trees)) |
|
| 117 |
-## } |
|
| 118 |
-## lapply(trees, read.stats_beast_internal, beast=beast) |
|
| 119 |
-## } |
|
| 120 |
- |
|
| 121 |
-## read.stats_beast_internal <- function(beast, tree) {
|
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| 122 |
-## tree2 <- gsub("\\[[^\\[]*\\]", "", tree)
|
|
| 123 |
-## phylo <- read.tree(text = tree2) |
|
| 124 |
- |
|
| 125 |
-## tree2 <- add_pseudo_nodelabel(phylo, tree2) |
|
| 126 |
- |
|
| 127 |
-## ## node name corresponding to stats |
|
| 128 |
-## nn <- strsplit(tree2, split=",") %>% unlist %>% |
|
| 129 |
-## strsplit(., split="\\)") %>% unlist %>% |
|
| 130 |
-## gsub("\\(*", "", .) %>%
|
|
| 131 |
-## gsub("[:;].*", "", .)
|
|
| 132 |
- |
|
| 133 |
-## phylo <- read.tree(text = tree2) |
|
| 134 |
-## root <- getRoot(phylo) |
|
| 135 |
-## nnode <- phylo$Nnode |
|
| 136 |
- |
|
| 137 |
-## ## phylo2 <- read.nexus(file) |
|
| 138 |
-## ## treeinfo <- fortify.phylo(phylo) |
|
| 139 |
-## ## treeinfo2 <- fortify.phylo(phylo2) |
|
| 140 |
-## ## treeinfo$label2 <- NA |
|
| 141 |
-## ## treeinfo$label2[treeinfo$isTip] <- treeinfo2$node[as.numeric(treeinfo$label[treeinfo$isTip])] |
|
| 142 |
-## ## treeinfo$visited <- FALSE |
|
| 143 |
-## ## root <- getRoot(phylo2) |
|
| 144 |
-## ## treeinfo[root, "visited"] <- TRUE |
|
| 145 |
-## ## currentNode <- 1:Ntip(phylo2) |
|
| 146 |
-## ## while(any(treeinfo$visited == FALSE)) {
|
|
| 147 |
-## ## pNode <- c() |
|
| 148 |
-## ## for (kk in currentNode) {
|
|
| 149 |
-## ## i <- which(treeinfo$label2 == kk) |
|
| 150 |
-## ## treeinfo[i, "visited"] <- TRUE |
|
| 151 |
-## ## j <- which(treeinfo2$node == kk) |
|
| 152 |
-## ## ip <- treeinfo$parent[i] |
|
| 153 |
-## ## if (ip != root) {
|
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| 154 |
-## ## ii <- which(treeinfo$node == ip) |
|
| 155 |
-## ## if (treeinfo$visited[ii] == FALSE) {
|
|
| 156 |
-## ## jp <- treeinfo2$parent[j] |
|
| 157 |
-## ## jj <- which(treeinfo2$node == jp) |
|
| 158 |
-## ## treeinfo[ii, "label2"] <- treeinfo2[jj, "node"] |
|
| 159 |
-## ## pNode <- c(pNode, jp) |
|
| 160 |
-## ## } |
|
| 161 |
-## ## treeinfo[ii, "visited"] <- TRUE |
|
| 162 |
-## ## } |
|
| 163 |
-## ## } |
|
| 164 |
-## ## currentNode <- unique(pNode) |
|
| 165 |
-## ## } |
|
| 166 |
-## ## treeinfo[root, "label2"] <- root |
|
| 167 |
-## ## ## convert nn to node that encoded in phylo2 |
|
| 168 |
-## ## node <- treeinfo$label2[match(nn, treeinfo$label)] |
|
| 169 |
- |
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| 170 |
- |
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| 171 |
-## #################################################### |
|
| 172 |
-## ## ## |
|
| 173 |
-## ## after doing it in the hard way ## |
|
| 174 |
-## ## I finally figure out the following easy way ## |
|
| 175 |
-## ## ## |
|
| 176 |
-## #################################################### |
|
| 177 |
-## treeinfo <- fortify.phylo(phylo) |
|
| 178 |
- |
|
| 179 |
-## if (any(grepl("TRANSLATE", beast, ignore.case = TRUE))) {
|
|
| 180 |
-## label2 <- c(treeinfo[treeinfo$isTip, "label"], |
|
| 181 |
-## root:(root+nnode-1)) |
|
| 182 |
-## node <- label2[match(nn, treeinfo$label)] |
|
| 183 |
-## } else {
|
|
| 184 |
-## node <- as.character(treeinfo$node[match(nn, treeinfo$label)]) |
|
| 185 |
-## } |
|
| 186 |
- |
|
| 187 |
-## ## stats <- unlist(strsplit(tree, "\\["))[-1] |
|
| 188 |
-## ## stats <- sub(":.+$", "", stats
|
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| 189 |
-## stats <- strsplit(tree, ":") %>% unlist |
|
| 190 |
-## names(stats) <- node |
|
| 191 |
-## stats <- stats[grep("\\[", stats)]
|
|
| 192 |
-## stats <- sub("[^\\[]+\\[", "", stats)
|
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| 193 |
- |
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| 194 |
-## stats <- sub("^&", "", stats)
|
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| 195 |
-## stats <- sub("];*$", "", stats)
|
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| 196 |
- |
|
| 197 |
-## stats2 <- lapply(stats, function(x) {
|
|
| 198 |
-## y <- unlist(strsplit(x, ",")) |
|
| 199 |
-## sidx <- grep("=\\{", y)
|
|
| 200 |
-## eidx <- grep("\\}$", y)
|
|
| 201 |
- |
|
| 202 |
-## flag <- FALSE |
|
| 203 |
-## if (length(sidx) > 0) {
|
|
| 204 |
-## flag <- TRUE |
|
| 205 |
-## SETS <- sapply(seq_along(sidx), function(k) {
|
|
| 206 |
-## p <- y[sidx[k]:eidx[k]] |
|
| 207 |
-## gsub(".*=\\{", "", p) %>% gsub("\\}$", "", .) %>% list
|
|
| 208 |
-## }) |
|
| 209 |
-## names(SETS) <- gsub("=.*", "", y[sidx])
|
|
| 210 |
- |
|
| 211 |
-## kk <- sapply(seq_along(sidx), function(k) sidx[k]:eidx[k]) %>% unlist |
|
| 212 |
-## y <- y[-kk] |
|
| 213 |
-## } |
|
| 214 |
- |
|
| 215 |
- |
|
| 216 |
-## name <- gsub("=.*", "", y)
|
|
| 217 |
-## val <- gsub(".*=", "", y) %>% gsub("^\\{", "", .) %>%
|
|
| 218 |
-## gsub("\\}$", "", .)
|
|
| 219 |
- |
|
| 220 |
- |
|
| 221 |
-## if (flag) {
|
|
| 222 |
-## nn <- c(name, names(SETS)) |
|
| 223 |
-## } else {
|
|
| 224 |
-## nn <- name |
|
| 225 |
-## } |
|
| 226 |
- |
|
| 227 |
-## res <- character(length(nn)) |
|
| 228 |
-## names(res) <- nn |
|
| 229 |
- |
|
| 230 |
-## for (i in seq_along(name)) {
|
|
| 231 |
-## res[i] <- val[i] |
|
| 232 |
-## } |
|
| 233 |
-## if (flag) {
|
|
| 234 |
-## j <- i |
|
| 235 |
-## for (i in seq_along(SETS)) {
|
|
| 236 |
-## res[i+j] <- SETS[i] |
|
| 237 |
-## } |
|
| 238 |
-## } |
|
| 239 |
- |
|
| 240 |
-## return(res) |
|
| 241 |
-## }) |
|
| 242 |
- |
|
| 243 |
-## nn <- lapply(stats2, names) %>% unlist %>% |
|
| 244 |
-## unique %>% sort |
|
| 245 |
- |
|
| 246 |
-## ## stats3 is a matrix |
|
| 247 |
-## stats3 <- t(sapply(stats2, function(x) {
|
|
| 248 |
-## for (ii in nn[!nn %in% names(x)]) {
|
|
| 249 |
-## x[ii] <- NA |
|
| 250 |
-## } |
|
| 251 |
-## x[nn] |
|
| 252 |
-## })) |
|
| 253 |
- |
|
| 254 |
-## stats3 <- as.data.frame(stats3) |
|
| 255 |
-## if (nrow(stats3) == 1) {
|
|
| 256 |
-## ## only has one evidence |
|
| 257 |
-## ## transpose |
|
| 258 |
-## stats3 <- data.frame(X=unlist(stats3[1,])) |
|
| 259 |
-## colnames(stats3) <- nn |
|
| 260 |
-## } |
|
| 261 |
-## colnames(stats3) <- gsub("(\\d+)%", "0.\\1", colnames(stats3))
|
|
| 262 |
- |
|
| 263 |
-## ## stats3$node <- node |
|
| 264 |
-## stats3$node <- names(stats) |
|
| 265 |
-## return(stats3) |
|
| 266 |
-## } |
|
| 267 |
- |
|
| 268 |
-## add_pseudo_nodelabel <- function(phylo, treetext) {
|
|
| 269 |
-## if(is.null(phylo$node.label)) {
|
|
| 270 |
-## nnode <- phylo$Nnode |
|
| 271 |
-## nlab <- paste("X", 1:nnode, sep="")
|
|
| 272 |
-## for (i in 1:nnode) {
|
|
| 273 |
-## treetext <- sub("\\)([:;])", paste0("\\)", nlab[i], "\\1"), treetext)
|
|
| 274 |
-## } |
|
| 275 |
-## } |
|
| 276 |
- |
|
| 277 |
-## return(treetext) |
|
| 278 |
-## } |
|
| 279 |
- |
|
| 280 |
- |
|
| 281 |
- |
| ... | ... |
@@ -18,7 +18,7 @@ |
| 18 | 18 |
##' require(ape) |
| 19 | 19 |
##' tr <- rtree(10) |
| 20 | 20 |
##' ggtree(tr) + geom_tiplab() |
| 21 |
-geom_tiplab <- function(mapping=NULL, hjust = 0, align = FALSE, linetype = "dotted", linesize=1, geom="text", offset = 0, ...) {
|
|
| 21 |
+geom_tiplab <- function(mapping=NULL, hjust = 0, align = FALSE, linetype = "dotted", linesize=1, geom="text", offset=0, ...) {
|
|
| 22 | 22 |
geom <- match.arg(geom, c("text", "label"))
|
| 23 | 23 |
if (geom == "text") {
|
| 24 | 24 |
text_geom <- geom_text2 |
| ... | ... |
@@ -43,6 +43,12 @@ geom_tiplab <- function(mapping=NULL, hjust = 0, align = FALSE, linetype = "dot |
| 43 | 43 |
show_segment <- FALSE |
| 44 | 44 |
if (align && (!is.na(linetype) && !is.null(linetype))) {
|
| 45 | 45 |
show_segment <- TRUE |
| 46 |
+ segment_mapping <- aes(x = max(x, na.rm=TRUE), |
|
| 47 |
+ xend = x + diff(range(x, na.rm=TRUE))/200, |
|
| 48 |
+ y = y, yend = y, |
|
| 49 |
+ subset=isTip) |
|
| 50 |
+ if (!is.null(mapping)) |
|
| 51 |
+ segment_mapping <- modifyList(segment_mapping, mapping) |
|
| 46 | 52 |
} |
| 47 | 53 |
|
| 48 | 54 |
list( |
| ... | ... |
@@ -50,10 +56,14 @@ geom_tiplab <- function(mapping=NULL, hjust = 0, align = FALSE, linetype = "dot |
| 50 | 56 |
hjust = hjust, nudge_x = offset, ...) |
| 51 | 57 |
, |
| 52 | 58 |
if (show_segment) |
| 53 |
- geom_tipsegment(mapping = aes(subset=isTip), |
|
| 54 |
- offset = offset, |
|
| 55 |
- linetype = linetype, |
|
| 56 |
- size = linesize, ...) |
|
| 59 |
+ geom_segment2(mapping = segment_mapping, |
|
| 60 |
+ linetype = linetype, |
|
| 61 |
+ size = linesize, ...) |
|
| 62 |
+ |
|
| 63 |
+ ## geom_tipsegment(mapping = segment_mapping, |
|
| 64 |
+ ## offset = offset, |
|
| 65 |
+ ## linetype = linetype, |
|
| 66 |
+ ## size = linesize, ...) |
|
| 57 | 67 |
) |
| 58 | 68 |
} |
| 59 | 69 |
|
| ... | ... |
@@ -88,47 +98,47 @@ geom_tiplab2 <- function(mapping=NULL, hjust=0, ...) {
|
| 88 | 98 |
) |
| 89 | 99 |
} |
| 90 | 100 |
|
| 91 |
-geom_tipsegment <- function(mapping=NULL, data=NULL, |
|
| 92 |
- geom=GeomSegmentGGtree, position = "identity", |
|
| 93 |
- offset, ..., |
|
| 94 |
- show.legend=NA, inherit.aes=FALSE, |
|
| 95 |
- na.rm=TRUE) {
|
|
| 96 |
- |
|
| 97 |
- default_aes <- aes_(x=~x, y=~y) |
|
| 98 |
- if (is.null(mapping)) {
|
|
| 99 |
- mapping <- default_aes |
|
| 100 |
- } else {
|
|
| 101 |
- mapping <- modifyList(default_aes, mapping) |
|
| 102 |
- } |
|
| 103 |
- |
|
| 104 |
- layer(stat=StatTipSegment, |
|
| 105 |
- data = data, |
|
| 106 |
- mapping = mapping, |
|
| 107 |
- geom = geom, |
|
| 108 |
- position = position, |
|
| 109 |
- show.legend = show.legend, |
|
| 110 |
- inherit.aes = inherit.aes, |
|
| 111 |
- params = list(offset = offset, |
|
| 112 |
- na.rm = na.rm, |
|
| 113 |
- ...), |
|
| 114 |
- check.aes = FALSE |
|
| 115 |
- ) |
|
| 116 |
-} |
|
| 117 |
- |
|
| 118 |
-StatTipSegment <- ggproto("StatTipSegment", Stat,
|
|
| 119 |
- compute_group = function(self, data, scales, params, offset) {
|
|
| 120 |
- get_tipsegment_position(data, offset) |
|
| 121 |
- }, |
|
| 122 |
- required_aes = c("x", "y")
|
|
| 123 |
- ) |
|
| 124 |
- |
|
| 125 |
- |
|
| 126 |
-get_tipsegment_position <- function(data, offset, adjustRatio=1/200) {
|
|
| 127 |
- adjust <- diff(range(data$x, na.rm=TRUE)) * adjustRatio |
|
| 128 |
- xend <- data$x + adjust |
|
| 129 |
- x <- max(data$x, na.rm = TRUE) + offset |
|
| 130 |
- y <- data$y |
|
| 131 |
- data.frame(x=x, xend=xend, y=y, yend=y) |
|
| 132 |
-} |
|
| 101 |
+## geom_tipsegment <- function(mapping=NULL, data=NULL, |
|
| 102 |
+## geom=GeomSegmentGGtree, position = "identity", |
|
| 103 |
+## offset, ..., |
|
| 104 |
+## show.legend=NA, inherit.aes=FALSE, |
|
| 105 |
+## na.rm=TRUE) {
|
|
| 106 |
+ |
|
| 107 |
+## default_aes <- aes_(x=~x, y=~y) |
|
| 108 |
+## if (is.null(mapping)) {
|
|
| 109 |
+## mapping <- default_aes |
|
| 110 |
+## } else {
|
|
| 111 |
+## mapping <- modifyList(default_aes, mapping) |
|
| 112 |
+## } |
|
| 113 |
+ |
|
| 114 |
+## layer(stat=StatTipSegment, |
|
| 115 |
+## data = data, |
|
| 116 |
+## mapping = mapping, |
|
| 117 |
+## geom = geom, |
|
| 118 |
+## position = position, |
|
| 119 |
+## show.legend = show.legend, |
|
| 120 |
+## inherit.aes = inherit.aes, |
|
| 121 |
+## params = list(offset = offset, |
|
| 122 |
+## na.rm = na.rm, |
|
| 123 |
+## ...), |
|
| 124 |
+## check.aes = FALSE |
|
| 125 |
+## ) |
|
| 126 |
+## } |
|
| 127 |
+ |
|
| 128 |
+## StatTipSegment <- ggproto("StatTipSegment", Stat,
|
|
| 129 |
+## compute_group = function(self, data, scales, params, offset) {
|
|
| 130 |
+## get_tipsegment_position(data, offset) |
|
| 131 |
+## }, |
|
| 132 |
+## required_aes = c("x", "y")
|
|
| 133 |
+## ) |
|
| 134 |
+ |
|
| 135 |
+ |
|
| 136 |
+## get_tipsegment_position <- function(data, offset, adjustRatio=1/200) {
|
|
| 137 |
+## adjust <- diff(range(data$x, na.rm=TRUE)) * adjustRatio |
|
| 138 |
+## xend <- data$x + adjust |
|
| 139 |
+## x <- max(data$x, na.rm = TRUE) + offset |
|
| 140 |
+## y <- data$y |
|
| 141 |
+## data.frame(x=x, xend=xend, y=y, yend=y) |
|
| 142 |
+## } |
|
| 133 | 143 |
|
| 134 | 144 |
|
| ... | ... |
@@ -1078,6 +1078,7 @@ getXcoord2 <- function(x, root, parent, child, len, start=0, rev=FALSE) {
|
| 1078 | 1078 |
if (rev == TRUE) {
|
| 1079 | 1079 |
direction <- -1 |
| 1080 | 1080 |
} |
| 1081 |
+ |
|
| 1081 | 1082 |
while(anyNA(x)) {
|
| 1082 | 1083 |
idx <- which(parent %in% currentNode) |
| 1083 | 1084 |
newNode <- child[idx] |
| ... | ... |
@@ -1186,9 +1187,15 @@ getYcoord <- function(tr, step=1) {
|
| 1186 | 1187 |
y[tip.idx] <- 1:Ntip * step |
| 1187 | 1188 |
y[-tip.idx] <- NA |
| 1188 | 1189 |
|
| 1190 |
+ ## use lookup table |
|
| 1191 |
+ pvec <- integer(max(tr$edge)) |
|
| 1192 |
+ pvec[child] = parent |
|
| 1193 |
+ |
|
| 1189 | 1194 |
currentNode <- 1:Ntip |
| 1190 | 1195 |
while(anyNA(y)) {
|
| 1191 |
- pNode <- unique(parent[child %in% currentNode]) |
|
| 1196 |
+ ## pNode <- unique(parent[child %in% currentNode]) |
|
| 1197 |
+ pNode <- unique(pvec[currentNode]) |
|
| 1198 |
+ |
|
| 1192 | 1199 |
## piping of magrittr is slower than nested function call. |
| 1193 | 1200 |
## pipeR is fastest, may consider to use pipeR |
| 1194 | 1201 |
## |
| ... | ... |
@@ -4,9 +4,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with |
| 4 | 4 |
|
| 5 | 5 |
<img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /> |
| 6 | 6 |
|
| 7 |
-[](https://bioconductor.org/packages/ggtree) [](https://github.com/guangchuangyu/ggtree) [](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) |
|
| 7 |
+[](https://bioconductor.org/packages/ggtree) [](https://github.com/guangchuangyu/ggtree) [](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) |
|
| 8 | 8 |
|
| 9 |
-[](http://www.repostatus.org/#active) [](https://codecov.io/gh/GuangchuangYu/ggtree) [](https://github.com/GuangchuangYu/ggtree/commits/master) [](https://github.com/GuangchuangYu/ggtree/network) [](https://github.com/GuangchuangYu/ggtree/stargazers) [](https://awesome-r.com/#awesome-r-graphic-displays) |
|
| 9 |
+[](http://www.repostatus.org/#active) [](https://codecov.io/gh/GuangchuangYu/ggtree) [](https://github.com/GuangchuangYu/ggtree/commits/master) [](https://github.com/GuangchuangYu/ggtree/network) [](https://github.com/GuangchuangYu/ggtree/stargazers) [](https://awesome-r.com/#awesome-r-graphic-displays) |
|
| 10 | 10 |
|
| 11 | 11 |
[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [](https://travis-ci.org/GuangchuangYu/ggtree) [](https://ci.appveyor.com/project/GuangchuangYu/ggtree) |
| 12 | 12 |
|
| ... | ... |
@@ -33,50 +33,50 @@ Please cite the following article when using `ggtree`: |
| 33 | 33 |
|
| 34 | 34 |
### Citation |
| 35 | 35 |
|
| 36 |
-[](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) |
|
| 36 |
+[](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) |
|
| 37 | 37 |
|
| 38 | 38 |
+-+---------+---------+---------+---------+---------+---+ |
| 39 |
- 15 + * + |
|
| 39 |
+ 20 + * + |
|
| 40 | 40 |
| | |
| 41 | 41 |
| | |
| 42 |
+ 15 + + |
|
| 42 | 43 |
| | |
| 43 |
- 10 + + |
|
| 44 | 44 |
| | |
| 45 |
+ 10 + + |
|
| 45 | 46 |
| | |
| 46 | 47 |
| | |
| 47 | 48 |
5 + + |
| 48 |
- | | |
|
| 49 | 49 |
| | |
| 50 | 50 |
| * | |
| 51 |
- +-+---------+---------+---------+---------+---------+---+ |
|
| 51 |
+ 0 +-+---------+---------+---------+---------+---------+---+ |
|
| 52 | 52 |
2016 2016.2 2016.4 2016.6 2016.8 2017 |
| 53 | 53 |
|
| 54 | 54 |
### Download stats |
| 55 | 55 |
|
| 56 |
-[](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) |
|
| 56 |
+[](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) |
|
| 57 | 57 |
|
| 58 |
- ++------------------+------------------+------------------+-----------------+-----------------+ |
|
| 59 |
- 3000 + * + |
|
| 58 |
+ ++------------------+-----------------+-----------------+-----------------+------------------++ |
|
| 59 |
+ 3000 + * + |
|
| 60 | 60 |
| | |
| 61 | 61 |
| | |
| 62 | 62 |
2500 + + |
| 63 | 63 |
| | |
| 64 | 64 |
| | |
| 65 | 65 |
| | |
| 66 |
- 2000 + * + |
|
| 67 |
- | * * * | |
|
| 68 |
- | * * | |
|
| 66 |
+ 2000 + * * + |
|
| 67 |
+ | * * * | |
|
| 68 |
+ | * * | |
|
| 69 | 69 |
1500 + + |
| 70 | 70 |
| | |
| 71 |
- | * | |
|
| 72 |
- | * * * * | |
|
| 73 |
- 1000 + * * + |
|
| 74 |
- | * * | |
|
| 75 |
- | * * * | |
|
| 71 |
+ | * | |
|
| 72 |
+ | * * * * | |
|
| 73 |
+ 1000 + * * + |
|
| 74 |
+ | * * | |
|
| 75 |
+ | * * * | |
|
| 76 | 76 |
| * | |
| 77 |
- 500 + * * + |
|
| 78 |
- | * * | |
|
| 77 |
+ 500 + * * + |
|
| 78 |
+ | * * | |
|
| 79 | 79 |
| * | |
| 80 | 80 |
0 + * * * + |
| 81 |
- ++------------------+------------------+------------------+-----------------+-----------------+ |
|
| 82 |
- 2015 2015.5 2016 2016.5 2017 |
|
| 81 |
+ ++------------------+-----------------+-----------------+-----------------+------------------++ |
|
| 82 |
+ 2015 2015.5 2016 2016.5 2017 2017.5 |
| ... | ... |
@@ -220,7 +220,7 @@ |
| 220 | 220 |
<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p> |
| 221 | 221 |
<p><a href="https://github.com/GuangchuangYu/featured_img">Let us know</a> if you have |
| 222 | 222 |
published using <code>ggtree</code> and your publication will be featured here.</p> |
| 223 |
-<p><a href="https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-16-blue.svg?style=flat" /></a></p> |
|
| 223 |
+<p><a href="https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-22-blue.svg?style=flat" /></a></p> |
|
| 224 | 224 |
<p><link rel='stylesheet' href=https://guangchuangyu.github.io/resume/css/morris.css> |
| 225 | 225 |
<script src='https://guangchuangyu.github.io/resume/css/jquery.min.js' type='text/javascript'></script> |
| 226 | 226 |
<script src='https://guangchuangyu.github.io/resume/css/raphael-min.js' type='text/javascript'></script> |
| ... | ... |
@@ -234,12 +234,12 @@ published using <code>ggtree</code> and your publication will be featured here.< |
| 234 | 234 |
height: 300px; |
| 235 | 235 |
}<br /> |
| 236 | 236 |
</style> |
| 237 |
-<div id="chart5a529be8ff3" class="rChart morris"></p> |
|
| 237 |
+<div id="chart5f2d37e8c08a" class="rChart morris"></p> |
|
| 238 | 238 |
</div> |
| 239 | 239 |
|
| 240 | 240 |
<script type='text/javascript'> |
| 241 | 241 |
var chartParams = {
|
| 242 |
- "element": "chart5a529be8ff3", |
|
| 242 |
+ "element": "chart5f2d37e8c08a", |
|
| 243 | 243 |
"width": 800, |
| 244 | 244 |
"height": 400, |
| 245 | 245 |
"xkey": "year", |
| ... | ... |
@@ -254,11 +254,11 @@ published using <code>ggtree</code> and your publication will be featured here.< |
| 254 | 254 |
}, |
| 255 | 255 |
{
|
| 256 | 256 |
"year": 2017, |
| 257 |
-"cites": 15, |
|
| 257 |
+"cites": 21, |
|
| 258 | 258 |
"pubid": "HtEfBTGE9r8C" |
| 259 | 259 |
} |
| 260 | 260 |
], |
| 261 |
-"id": "chart5a529be8ff3", |
|
| 261 |
+"id": "chart5f2d37e8c08a", |
|
| 262 | 262 |
"labels": "cites" |
| 263 | 263 |
}, |
| 264 | 264 |
chartType = "Bar" |
| ... | ... |
@@ -218,7 +218,7 @@ |
| 218 | 218 |
<!-- AddToAny END --> |
| 219 | 219 |
|
| 220 | 220 |
<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p> |
| 221 |
-<p><a href="https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-16-blue.svg?style=flat" /></a></p> |
|
| 221 |
+<p><a href="https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-22-blue.svg?style=flat" /></a></p> |
|
| 222 | 222 |
<!-- citation:=HtEfBTGE9r8C:=7268358477862164627 --> |
| 223 | 223 |
|
| 224 | 224 |
<h2 id="journal-articles"><i class="fa fa-mortar-board"></i> Journal Articles</h2> |
| ... | ... |
@@ -232,10 +232,10 @@ |
| 232 | 232 |
<p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p> |
| 233 | 233 |
<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"> |
| 234 | 234 |
<link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css"></p> |
| 235 |
-<p><a href="https://bioconductor.org/packages/ggtree"><img alt="" src="https://img.shields.io/badge/release%20version-1.8.0-blue.svg?style=flat" /></a> |
|
| 236 |
-<a href="https://github.com/guangchuangyu/ggtree"><img alt="" src="https://img.shields.io/badge/devel%20version-1.9.0-blue.svg?style=flat" /></a> |
|
| 237 |
-<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-14716/total-blue.svg?style=flat" /></a> |
|
| 238 |
-<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-1385/month-blue.svg?style=flat" /></a></p> |
|
| 235 |
+<p><a href="https://bioconductor.org/packages/ggtree"><img alt="" src="https://img.shields.io/badge/release%20version-1.8.1-blue.svg?style=flat" /></a> |
|
| 236 |
+<a href="https://github.com/guangchuangyu/ggtree"><img alt="" src="https://img.shields.io/badge/devel%20version-1.9.1-blue.svg?style=flat" /></a> |
|
| 237 |
+<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-16372/total-blue.svg?style=flat" /></a> |
|
| 238 |
+<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-1117/month-blue.svg?style=flat" /></a></p> |
|
| 239 | 239 |
<p>The <code>ggtree</code> package extending the <em>ggplot2</em> package. It based on |
| 240 | 240 |
grammar of graphics and takes all the good parts of <em>ggplot2</em>. <em>ggtree</em> |
| 241 | 241 |
is designed for not only viewing phylogenetic tree but also displaying |
| ... | ... |
@@ -256,8 +256,8 @@ University of Hong Kong.</p> |
| 256 | 256 |
<h2 id="citation"><i class="fa fa-book"></i> Citation</h2> |
| 257 | 257 |
<p>Please cite the following article when using <code>ggtree</code>:</p> |
| 258 | 258 |
<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img alt="" src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" /></a> |
| 259 |
-<a href="https://www.altmetric.com/details/10533079"><img alt="" src="https://img.shields.io/badge/Altmetric-347-blue.svg?style=flat" /></a> |
|
| 260 |
-<a href="https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-16-blue.svg?style=flat" /></a></p> |
|
| 259 |
+<a href="https://www.altmetric.com/details/10533079"><img alt="" src="https://img.shields.io/badge/Altmetric-346-blue.svg?style=flat" /></a> |
|
| 260 |
+<a href="https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-22-blue.svg?style=flat" /></a></p> |
|
| 261 | 261 |
<p><strong>G Yu</strong>, DK Smith, H Zhu, Y Guan, TTY Lam<sup>*</sup>. ggtree: an R |
| 262 | 262 |
package for visualization and annotation of phylogenetic trees with |
| 263 | 263 |
their covariates and other associated data. <strong><em>Methods in Ecology and |
| ... | ... |
@@ -217,7 +217,7 @@ |
| 217 | 217 |
}, |
| 218 | 218 |
{
|
| 219 | 219 |
"location": "/featuredArticles/", |
| 220 |
- "text": "Let us know\n if you have\npublished using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n .rChart {\n display: block;\n margin-left: auto; \n margin-right: auto;\n width: 800px;\n height: 300px;\n }<br />\n \n\n\n\n\n\n\n\n\n var chartParams = {\n \"element\": \"chart5a529be8ff3\",\n\"width\": 800,\n\"height\": 400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\": 1,\n\"pubid\": \"HtEfBTGE9r8C\" \n},\n{\n \"year\": 2017,\n\"cites\": 15,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart5a529be8ff3\",\n\"labels\": \"cites\" \n},\n chartType = \"Bar\"\n new Morris[chartType](chartParams)\n\n\n\n\n\n\n\n\n\n\n 2017\n\n\nPhylogenetic analysis of the human antibody repertoire reveals\nquantitative signatures of immune senescence and\naging\n. \nPNAS\n, 2017\n\n\nHorses in Denmark Are a Reservoir of Diverse Clones of\nMethicillin-Resistant and -Susceptible Staphylococcus\naureus\n.\n\nFrontiers in Microbiology\n, 2017, 8:543\n\n\nGut metagenomes of type 2 diabetic patients have characteristic\nsingle-nucleotide polymorphism distribution in \nBacteroides\ncoprocola\n.\n\nMicrobiome\n, 2017, 5:15\n\n\n 2016\n\n\nFunction and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate\nTransferases and Their Diversity in the Proximal Colon of\nSwine\n. \nApplied and\nEnvironmental Microbiology\n. 2016, 82(22):6788-6798.",
|
|
| 220 |
+ "text": "Let us know\n if you have\npublished using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n .rChart {\n display: block;\n margin-left: auto; \n margin-right: auto;\n width: 800px;\n height: 300px;\n }<br />\n \n\n\n\n\n\n\n\n\n var chartParams = {\n \"element\": \"chart5f2d37e8c08a\",\n\"width\": 800,\n\"height\": 400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\": 1,\n\"pubid\": \"HtEfBTGE9r8C\" \n},\n{\n \"year\": 2017,\n\"cites\": 21,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart5f2d37e8c08a\",\n\"labels\": \"cites\" \n},\n chartType = \"Bar\"\n new Morris[chartType](chartParams)\n\n\n\n\n\n\n\n\n\n\n 2017\n\n\nPhylogenetic analysis of the human antibody repertoire reveals\nquantitative signatures of immune senescence and\naging\n. \nPNAS\n, 2017\n\n\nHorses in Denmark Are a Reservoir of Diverse Clones of\nMethicillin-Resistant and -Susceptible Staphylococcus\naureus\n.\n\nFrontiers in Microbiology\n, 2017, 8:543\n\n\nGut metagenomes of type 2 diabetic patients have characteristic\nsingle-nucleotide polymorphism distribution in \nBacteroides\ncoprocola\n.\n\nMicrobiome\n, 2017, 5:15\n\n\n 2016\n\n\nFunction and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate\nTransferases and Their Diversity in the Proximal Colon of\nSwine\n. \nApplied and\nEnvironmental Microbiology\n. 2016, 82(22):6788-6798.",
|
|
| 221 | 221 |
"title": "Featured Articles" |
| 222 | 222 |
}, |
| 223 | 223 |
{
|
| ... | ... |
@@ -4,7 +4,7 @@ |
| 4 | 4 |
|
| 5 | 5 |
<url> |
| 6 | 6 |
<loc>https://guangchuangyu.github.io/ggtree/</loc> |
| 7 |
- <lastmod>2017-04-30</lastmod> |
|
| 7 |
+ <lastmod>2017-06-19</lastmod> |
|
| 8 | 8 |
<changefreq>daily</changefreq> |
| 9 | 9 |
</url> |
| 10 | 10 |
|
| ... | ... |
@@ -12,7 +12,7 @@ |
| 12 | 12 |
|
| 13 | 13 |
<url> |
| 14 | 14 |
<loc>https://guangchuangyu.github.io/ggtree/documentation/</loc> |
| 15 |
- <lastmod>2017-04-30</lastmod> |
|
| 15 |
+ <lastmod>2017-06-19</lastmod> |
|
| 16 | 16 |
<changefreq>daily</changefreq> |
| 17 | 17 |
</url> |
| 18 | 18 |
|
| ... | ... |
@@ -20,7 +20,7 @@ |
| 20 | 20 |
|
| 21 | 21 |
<url> |
| 22 | 22 |
<loc>https://guangchuangyu.github.io/ggtree/faq/</loc> |
| 23 |
- <lastmod>2017-04-30</lastmod> |
|
| 23 |
+ <lastmod>2017-06-19</lastmod> |
|
| 24 | 24 |
<changefreq>daily</changefreq> |
| 25 | 25 |
</url> |
| 26 | 26 |
|
| ... | ... |
@@ -28,7 +28,7 @@ |
| 28 | 28 |
|
| 29 | 29 |
<url> |
| 30 | 30 |
<loc>https://guangchuangyu.github.io/ggtree/featuredArticles/</loc> |
| 31 |
- <lastmod>2017-04-30</lastmod> |
|
| 31 |
+ <lastmod>2017-06-19</lastmod> |
|
| 32 | 32 |
<changefreq>daily</changefreq> |
| 33 | 33 |
</url> |
| 34 | 34 |
|
| ... | ... |
@@ -36,7 +36,7 @@ |
| 36 | 36 |
|
| 37 | 37 |
<url> |
| 38 | 38 |
<loc>https://guangchuangyu.github.io/ggtree/gallery/</loc> |
| 39 |
- <lastmod>2017-04-30</lastmod> |
|
| 39 |
+ <lastmod>2017-06-19</lastmod> |
|
| 40 | 40 |
<changefreq>daily</changefreq> |
| 41 | 41 |
</url> |
| 42 | 42 |
|
| ... | ... |
@@ -45,55 +45,55 @@ |
| 45 | 45 |
|
| 46 | 46 |
<url> |
| 47 | 47 |
<loc>https://guangchuangyu.github.io/ggtree/ChIPseeker/</loc> |
| 48 |
- <lastmod>2017-04-30</lastmod> |
|
| 48 |
+ <lastmod>2017-06-19</lastmod> |
|
| 49 | 49 |
<changefreq>daily</changefreq> |
| 50 | 50 |
</url> |
| 51 | 51 |
|
| 52 | 52 |
<url> |
| 53 | 53 |
<loc>https://guangchuangyu.github.io/ggtree/clusterProfiler/</loc> |
| 54 |
- <lastmod>2017-04-30</lastmod> |
|
| 54 |
+ <lastmod>2017-06-19</lastmod> |
|
| 55 | 55 |
<changefreq>daily</changefreq> |
| 56 | 56 |
</url> |
| 57 | 57 |
|
| 58 | 58 |
<url> |
| 59 | 59 |
<loc>https://guangchuangyu.github.io/ggtree/DOSE/</loc> |
| 60 |
- <lastmod>2017-04-30</lastmod> |
|
| 60 |
+ <lastmod>2017-06-19</lastmod> |
|
| 61 | 61 |
<changefreq>daily</changefreq> |
| 62 | 62 |
</url> |
| 63 | 63 |
|
| 64 | 64 |
<url> |
| 65 | 65 |
<loc>https://guangchuangyu.github.io/ggtree/emojifont/</loc> |
| 66 |
- <lastmod>2017-04-30</lastmod> |
|
| 66 |
+ <lastmod>2017-06-19</lastmod> |
|
| 67 | 67 |
<changefreq>daily</changefreq> |
| 68 | 68 |
</url> |
| 69 | 69 |
|
| 70 | 70 |
<url> |
| 71 | 71 |
<loc>https://guangchuangyu.github.io/ggtree/ggtree/</loc> |
| 72 |
- <lastmod>2017-04-30</lastmod> |
|
| 72 |
+ <lastmod>2017-06-19</lastmod> |
|
| 73 | 73 |
<changefreq>daily</changefreq> |
| 74 | 74 |
</url> |
| 75 | 75 |
|
| 76 | 76 |
<url> |
| 77 | 77 |
<loc>https://guangchuangyu.github.io/ggtree/GOSemSim/</loc> |
| 78 |
- <lastmod>2017-04-30</lastmod> |
|
| 78 |
+ <lastmod>2017-06-19</lastmod> |
|
| 79 | 79 |
<changefreq>daily</changefreq> |
| 80 | 80 |
</url> |
| 81 | 81 |
|
| 82 | 82 |
<url> |
| 83 | 83 |
<loc>https://guangchuangyu.github.io/ggtree/meshes/</loc> |
| 84 |
- <lastmod>2017-04-30</lastmod> |
|
| 84 |
+ <lastmod>2017-06-19</lastmod> |
|
| 85 | 85 |
<changefreq>daily</changefreq> |
| 86 | 86 |
</url> |
| 87 | 87 |
|
| 88 | 88 |
<url> |
| 89 | 89 |
<loc>https://guangchuangyu.github.io/ggtree/ReactomePA/</loc> |
| 90 |
- <lastmod>2017-04-30</lastmod> |
|
| 90 |
+ <lastmod>2017-06-19</lastmod> |
|
| 91 | 91 |
<changefreq>daily</changefreq> |
| 92 | 92 |
</url> |
| 93 | 93 |
|
| 94 | 94 |
<url> |
| 95 | 95 |
<loc>https://guangchuangyu.github.io/ggtree/treeio/</loc> |
| 96 |
- <lastmod>2017-04-30</lastmod> |
|
| 96 |
+ <lastmod>2017-06-19</lastmod> |
|
| 97 | 97 |
<changefreq>daily</changefreq> |
| 98 | 98 |
</url> |
| 99 | 99 |
|
| ... | ... |
@@ -24,7 +24,7 @@ output: |
| 24 | 24 |
[Let us know](https://github.com/GuangchuangYu/featured_img) if you have |
| 25 | 25 |
published using `ggtree` and your publication will be featured here. |
| 26 | 26 |
|
| 27 |
-[](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) |
|
| 27 |
+[](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) |
|
| 28 | 28 |
|
| 29 | 29 |
<link rel='stylesheet' href=https://guangchuangyu.github.io/resume/css/morris.css> |
| 30 | 30 |
<script src='https://guangchuangyu.github.io/resume/css/jquery.min.js' type='text/javascript'></script> |
| ... | ... |
@@ -39,13 +39,13 @@ published using `ggtree` and your publication will be featured here. |
| 39 | 39 |
height: 300px; |
| 40 | 40 |
} |
| 41 | 41 |
</style> |
| 42 |
-<div id="chart5a529be8ff3" class="rChart morris"> |
|
| 42 |
+<div id="chart5f2d37e8c08a" class="rChart morris"> |
|
| 43 | 43 |
|
| 44 | 44 |
</div> |
| 45 | 45 |
|
| 46 | 46 |
<script type='text/javascript'> |
| 47 | 47 |
var chartParams = {
|
| 48 |
- "element": "chart5a529be8ff3", |
|
| 48 |
+ "element": "chart5f2d37e8c08a", |
|
| 49 | 49 |
"width": 800, |
| 50 | 50 |
"height": 400, |
| 51 | 51 |
"xkey": "year", |
| ... | ... |
@@ -60,11 +60,11 @@ published using `ggtree` and your publication will be featured here. |
| 60 | 60 |
}, |
| 61 | 61 |
{
|
| 62 | 62 |
"year": 2017, |
| 63 |
-"cites": 15, |
|
| 63 |
+"cites": 21, |
|
| 64 | 64 |
"pubid": "HtEfBTGE9r8C" |
| 65 | 65 |
} |
| 66 | 66 |
], |
| 67 |
-"id": "chart5a529be8ff3", |
|
| 67 |
+"id": "chart5f2d37e8c08a", |
|
| 68 | 68 |
"labels": "cites" |
| 69 | 69 |
}, |
| 70 | 70 |
chartType = "Bar" |
| ... | ... |
@@ -21,7 +21,7 @@ output: |
| 21 | 21 |
<!-- AddToAny END --> |
| 22 | 22 |
<link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"> |
| 23 | 23 |
|
| 24 |
-[](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) |
|
| 24 |
+[](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) |
|
| 25 | 25 |
|
| 26 | 26 |
<!-- citation:=HtEfBTGE9r8C:=7268358477862164627 --> |
| 27 | 27 |
<i class="fa fa-mortar-board"></i> Journal Articles |
| ... | ... |
@@ -27,10 +27,10 @@ ggtree: visualization and annotation of phylogenetic trees |
| 27 | 27 |
<link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"> |
| 28 | 28 |
<link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css"> |
| 29 | 29 |
|
| 30 |
-[](https://bioconductor.org/packages/ggtree) |
|
| 31 |
-[](https://github.com/guangchuangyu/ggtree) |
|
| 32 |
-[](https://bioconductor.org/packages/stats/bioc/ggtree) |
|
| 33 |
-[](https://bioconductor.org/packages/stats/bioc/ggtree) |
|
| 30 |
+[](https://bioconductor.org/packages/ggtree) |
|
| 31 |
+[](https://github.com/guangchuangyu/ggtree) |
|
| 32 |
+[](https://bioconductor.org/packages/stats/bioc/ggtree) |
|
| 33 |
+[](https://bioconductor.org/packages/stats/bioc/ggtree) |
|
| 34 | 34 |
|
| 35 | 35 |
The `ggtree` package extending the *ggplot2* package. It based on |
| 36 | 36 |
grammar of graphics and takes all the good parts of *ggplot2*. *ggtree* |
| ... | ... |
@@ -60,8 +60,8 @@ University of Hong Kong. |
| 60 | 60 |
Please cite the following article when using `ggtree`: |
| 61 | 61 |
|
| 62 | 62 |
[](http://dx.doi.org/10.1111/2041-210X.12628) |
| 63 |
-[](https://www.altmetric.com/details/10533079) |
|
| 64 |
-[](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) |
|
| 63 |
+[](https://www.altmetric.com/details/10533079) |
|
| 64 |
+[](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) |
|
| 65 | 65 |
|
| 66 | 66 |
**G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R |
| 67 | 67 |
package for visualization and annotation of phylogenetic trees with |
