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

     R (>= 3.5.0)

 Imports:

     ape,

-    aplot (>= 0.1.3),

+    aplot,

     dplyr,

     ggplot2 (>= 3.0.0),

     grid,

@@ -31,7 +31,7 @@ Imports:

     methods,

     purrr,

     rlang,

-    ggfun,

+    ggfun (>= 0.0.6),

     yulab.utils,

     tidyr,

     tidytree (>= 0.3.9),

@@ -37,7 +37,6 @@ S3method(ggplot_add,tree_inset)

 S3method(ggplot_add,zoom_clade)

 S3method(groupClade,ggtree)

 S3method(groupOTU,ggtree)

-S3method(identify,gg)

 S3method(nodeid,ggtree)

 S3method(nodelab,ggtree)

 S3method(offspring,ggtree)

@@ -108,6 +107,7 @@ export(groupOTU)

 export(guide_legend)

 export(gzoom)

 export(hexpand)

+export(identify)

 export(inset)

 export(label_pad)

 export(layout_circular)

@@ -173,6 +173,7 @@ importFrom(dplyr,mutate)

 importFrom(dplyr,rename)

 importFrom(dplyr,select)

 importFrom(ggfun,get_aes_var)

+importFrom(ggfun,identify)

 importFrom(ggplot2,Geom)

 importFrom(ggplot2,GeomLabel)

 importFrom(ggplot2,GeomPoint)

@@ -241,16 +242,11 @@ importFrom(ggplot2,xlab)

 importFrom(ggplot2,xlim)

 importFrom(ggplot2,ylab)

 importFrom(ggplot2,ylim)

-importFrom(graphics,identify)

 importFrom(grid,arrow)

-importFrom(grid,convertX)

-importFrom(grid,convertY)

 importFrom(grid,curveGrob)

-importFrom(grid,dataViewport)

 importFrom(grid,gTree)

 importFrom(grid,gpar)

 importFrom(grid,grid.layout)

-importFrom(grid,grid.locator)

 importFrom(grid,grid.newpage)

 importFrom(grid,grobTree)

 importFrom(grid,pushViewport)

@@ -27,7 +27,8 @@

 # ggtree 3.3.1.901

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

++ mv `identify()` method to 'ggfun' (2022-04-01, Fri)

++ update `identify.gg()` to support 'ggplot' object and `+xlim()` 

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

 # ggtree 3.3.1

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

 }

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

-    r <- ggrange(plot, var)

+    r <- ggfun::ggrange(plot, var)

     rr <- diff(r)

     if (direction == 1) {

         res <- r[2] + rr * ratio

deleted file mode 100644

@@ -1,61 +0,0 @@

-

-##' identify node by interactive click

-##'

-##'

-##' @rdname identify

-##' @title identify

-##' @param x tree view

-##' @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

-##' @importFrom grid grid.locator

-##' @importFrom grid unit

-##' @importFrom grid dataViewport

-##' @importFrom graphics identify

-##' @importFrom ggplot2 last_plot

-##' @method identify gg

-##' @export

-##' @author Guangchuang Yu

-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

-

-    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

-

-    xx <- as.numeric(convertX( unit(x,'native'), 'in' ))

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

-

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

-    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)

-}

-

@@ -106,3 +106,7 @@ grid::unit

 ##' @importFrom aplot plot_list

 ##' @export

 aplot::plot_list

+

+##' @importFrom ggfun identify

+##' @export

+ggfun::identify

@@ -175,5 +175,5 @@ message_wrap <- function(...){

 ## }

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

+

deleted file mode 100644

@@ -1,24 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/method-identify.R

-\name{identify.gg}

-\alias{identify.gg}

-\title{identify}

-\usage{

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

-}

-\arguments{

-\item{x}{tree view}

-

-\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{

-closest data point

-}

-\description{

-identify node by interactive click

-}

-\author{

-Guangchuang Yu

-}

@@ -30,6 +30,7 @@

 \alias{arrow}

 \alias{unit}

 \alias{plot_list}

+\alias{identify}

 \title{Objects exported from other packages}

 \keyword{internal}

 \description{

@@ -43,6 +44,8 @@ below to see their documentation.

   \item{dplyr}{\code{\link[dplyr:compute]{collapse}}}

+  \item{ggfun}{\code{\link[ggfun:reexports]{identify}}}

+

   \item{ggplot2}{\code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{fortify}}, \code{\link[ggplot2:geom_text]{geom_label}}, \code{\link[ggplot2]{geom_point}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{guide_legend}}, \code{\link[ggplot2:element]{margin}}, \code{\link[ggplot2:scale_manual]{scale_color_manual}}, \code{\link[ggplot2:scale_manual]{scale_colour_manual}}, \code{\link[ggplot2:scale_manual]{scale_fill_manual}}, \code{\link[ggplot2:scale_continuous]{scale_x_continuous}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2:lims]{xlim}}}

   \item{grid}{\code{\link[grid]{arrow}}, \code{\link[grid]{unit}}}