@@ -1,7 +1,7 @@

 Package: ggtree

 Type: Package

 Title: an R package for visualization of tree and annotation data

-Version: 3.3.1.900

+Version: 3.3.1.901

 Authors@R: c(

        person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), 

             comment = c(ORCID = "0000-0002-6485-8781")),

@@ -23,7 +23,7 @@ Depends:

     R (>= 3.5.0)

 Imports:

     ape,

-    aplot (>= 0.0.4),

+    aplot (>= 0.1.3),

     dplyr,

     ggplot2 (>= 3.0.0),

     grid,

@@ -25,8 +25,9 @@

 -->

-# ggtree 3.3.1.900

+# ggtree 3.3.1.901

++ update `identify.gg()` to support 'ggplot' object and `+xlim()` (2022-04-01, Fri)

 + update man files (2022-03-23, Wed, #489)

 # ggtree 3.3.1

@@ -120,12 +120,3 @@ revts <- function(treeview) {

     treeview

 }

-

-ggrange2 <- function(plot, var) {

-    ## aplot::ggrange extract panel range

-    ## this function extract plot range

-

-    var <- paste0("panel_scales_", var)

-    ggplot_build(plot)$layout[[var]][[1]]$range$range

-}

-

@@ -159,7 +159,7 @@ ggplot_add.ggexpand <- function(object, plot, object_name) {

 }

 ggexpand_internal <- function(plot, ratio, direction, var) {

-    r <- ggrange2(plot, var)

+    r <- ggrange(plot, var)

     rr <- diff(r)

     if (direction == 1) {

         res <- r[2] + rr * ratio

@@ -5,8 +5,9 @@

 ##' @rdname identify

 ##' @title identify

 ##' @param x tree view

-##' @param ... additional parameters

-##' @return node id

+##' @param col selected columns to extract. Default is "auto" which will select all columns for 'ggplot' object and 'node' column for 'ggtree' object

+##' @param ... additional parameters, normally ignored

+##' @return closest data point

 ##' @importFrom grid convertX

 ##' @importFrom grid convertY

 ##' @importFrom grid pushViewport

@@ -18,12 +19,23 @@

 ##' @method identify gg

 ##' @export

 ##' @author Guangchuang Yu

-identify.gg <- function(x = last_plot(), ...) {

-    tree_view <- x

+identify.gg <- function(x = last_plot(), col = "auto", ...) {

+    ## tree_view <- x

     ## x=NULL, it will call graphics::identify

-    x <- tree_view$data$x

-    y <- tree_view$data$y

+    ## x <- tree_view$data$x

+    ## y <- tree_view$data$y

+

+    plot <- x

+    xvar <- ggfun::get_aes_var(plot$mapping, 'x')

+    yvar <- ggfun::get_aes_var(plot$mapping, 'y')

+    x <- plot$data[[xvar]]

+    y <- plot$data[[yvar]]

+

+    xlim <- aplot::xrange(plot)

+    ylim <- aplot::yrange(plot)

+    x <- c(x, rep(xlim, times = 2))

+    y <- c(y, rep(ylim, each = 2))

     pushViewport(dataViewport(x, y))

     loc <- grid.locator('in') %>% as.numeric

@@ -32,6 +44,18 @@ identify.gg <- function(x = last_plot(), ...) {

     yy <- as.numeric(convertY( unit(y,'native'), 'in' ))

     idx <- which.min( (xx-loc[1])^2 + (yy-loc[2])^2 )

-    return(tree_view$data$node[idx])

+    res <- plot$data[idx,]

+    if (col == "auto" && inherits(plot, 'ggtree')) {

+        col <- 'node'

+    }

+    if (length(col) == 1 && col == "auto") {

+        return(res)

+    }

+

+    res <- res[,col]

+    if (length(col) == 1) {

+        res <- res[[1]]

+    }

+    return(res)

 }

@@ -173,3 +173,7 @@ message_wrap <- function(...){

 ##     tree$edge.length <- c(tree$edge.length, rep(0, ii))

 ##     return(tree)

 ## }

+

+

+ggrange <- getFromNamespace("ggrange", "aplot")

+

@@ -4,15 +4,17 @@

 \alias{identify.gg}

 \title{identify}

 \usage{

-\method{identify}{gg}(x = last_plot(), ...)

+\method{identify}{gg}(x = last_plot(), col = "auto", ...)

 }

 \arguments{

 \item{x}{tree view}

-\item{...}{additional parameters}

+\item{col}{selected columns to extract. Default is "auto" which will select all columns for 'ggplot' object and 'node' column for 'ggtree' object}

+

+\item{...}{additional parameters, normally ignored}

 }

 \value{

-node id

+closest data point

 }

 \description{

 identify node by interactive click