1. ggtree
  2. R
  3. method-identify.R
Browse code

mv identify to ggfun

Guangchuang Yu authored on 01/04/2022 08:21:52
Showing 1 changed files
R/method-identify.R
History View file @ 7e05bcf0
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deleted file mode 100644
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@@ -1,61 +0,0 @@
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-
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-##' identify node by interactive click
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-##'
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-##'
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-##' @rdname identify
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-##' @title identify
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-##' @param x tree view
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-##' @param col selected columns to extract. Default is "auto" which will select all columns for 'ggplot' object and 'node' column for 'ggtree' object
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-##' @param ... additional parameters, normally ignored
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-##' @return closest data point
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-##' @importFrom grid convertX
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-##' @importFrom grid convertY
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-##' @importFrom grid pushViewport
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-##' @importFrom grid grid.locator
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-##' @importFrom grid unit
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-##' @importFrom grid dataViewport
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-##' @importFrom graphics identify
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-##' @importFrom ggplot2 last_plot
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-##' @method identify gg
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-##' @export
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-##' @author Guangchuang Yu
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-identify.gg <- function(x = last_plot(), col = "auto", ...) {
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-    ## tree_view <- x
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-    ## x=NULL, it will call graphics::identify
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-
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-    ## x <- tree_view$data$x
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-    ## y <- tree_view$data$y
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-
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-    plot <- x
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-    xvar <- ggfun::get_aes_var(plot$mapping, 'x')
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-    yvar <- ggfun::get_aes_var(plot$mapping, 'y')
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-    x <- plot$data[[xvar]]
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-    y <- plot$data[[yvar]]
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-
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-    xlim <- aplot::xrange(plot)
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-    ylim <- aplot::yrange(plot)
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-    x <- c(x, rep(xlim, times = 2))
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-    y <- c(y, rep(ylim, each = 2))
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-
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-    pushViewport(dataViewport(x, y))
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-    loc <- grid.locator('in') %>% as.numeric
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-
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-    xx <- as.numeric(convertX( unit(x,'native'), 'in' ))
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-    yy <- as.numeric(convertY( unit(y,'native'), 'in' ))
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-
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-    idx <- which.min( (xx-loc[1])^2 + (yy-loc[2])^2 )
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-    res <- plot$data[idx,]
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-    if (col == "auto" && inherits(plot, 'ggtree')) {
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-        col <- 'node'
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-    }
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-    if (length(col) == 1 && col == "auto") {
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-        return(res)
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-    }
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-
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-    res <- res[,col]
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-    if (length(col) == 1) {
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-        res <- res[[1]]
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-    }
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-    return(res)
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-}
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-
Browse code

update identify() method

Guangchuang Yu authored on 01/04/2022 02:45:58
Showing 1 changed files
R/method-identify.R
History View file @ c94a8385
... ... 
@@ -5,8 +5,9 @@
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 ##' @rdname identify
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 ##' @title identify
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 ##' @param x tree view
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-##' @param ... additional parameters
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-##' @return node id
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+##' @param col selected columns to extract. Default is "auto" which will select all columns for 'ggplot' object and 'node' column for 'ggtree' object
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+##' @param ... additional parameters, normally ignored
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+##' @return closest data point
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 ##' @importFrom grid convertX
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 ##' @importFrom grid convertY
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 ##' @importFrom grid pushViewport
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@@ -18,12 +19,23 @@
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 ##' @method identify gg
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 ##' @export
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 ##' @author Guangchuang Yu
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-identify.gg <- function(x = last_plot(), ...) {
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-    tree_view <- x
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+identify.gg <- function(x = last_plot(), col = "auto", ...) {
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+    ## tree_view <- x
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     ## x=NULL, it will call graphics::identify
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-    x <- tree_view$data$x
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-    y <- tree_view$data$y
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+    ## x <- tree_view$data$x
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+    ## y <- tree_view$data$y
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+
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+    plot <- x
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+    xvar <- ggfun::get_aes_var(plot$mapping, 'x')
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+    yvar <- ggfun::get_aes_var(plot$mapping, 'y')
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+    x <- plot$data[[xvar]]
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+    y <- plot$data[[yvar]]
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+
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+    xlim <- aplot::xrange(plot)
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+    ylim <- aplot::yrange(plot)
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+    x <- c(x, rep(xlim, times = 2))
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+    y <- c(y, rep(ylim, each = 2))
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     pushViewport(dataViewport(x, y))
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     loc <- grid.locator('in') %>% as.numeric
... ... 
@@ -32,6 +44,18 @@ identify.gg <- function(x = last_plot(), ...) {
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     yy <- as.numeric(convertY( unit(y,'native'), 'in' ))
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     idx <- which.min( (xx-loc[1])^2 + (yy-loc[2])^2 )
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-    return(tree_view$data$node[idx])
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+    res <- plot$data[idx,]
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+    if (col == "auto" && inherits(plot, 'ggtree')) {
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+        col <- 'node'
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+    }
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+    if (length(col) == 1 && col == "auto") {
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+        return(res)
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+    }
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+
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+    res <- res[,col]
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+    if (length(col) == 1) {
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+        res <- res[[1]]
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+    }
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+    return(res)
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 }
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Browse code

geom_range

Guangchuang Yu authored on 23/07/2019 16:25:05
Showing 1 changed files
R/method-identify.R
History View file @ 1418c053
... ... 
@@ -14,13 +14,13 @@
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 ##' @importFrom grid unit
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 ##' @importFrom grid dataViewport
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 ##' @importFrom graphics identify
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+##' @importFrom ggplot2 last_plot
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 ##' @method identify gg
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 ##' @export
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 ##' @author Guangchuang Yu
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-identify.gg <- function(x, ...) {
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+identify.gg <- function(x = last_plot(), ...) {
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     tree_view <- x
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-    ## not used, since if x=NULL, it will call graphics::identify
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-    ## tree_view %<>% get_tree_view
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+    ## x=NULL, it will call graphics::identify
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     x <- tree_view$data$x
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     y <- tree_view$data$y
Browse code

identify method for ggtree

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@118985 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 28/06/2016 06:26:04
Showing 1 changed files
R/method-identify.R
History View file @ 9e9bcff3
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new file mode 100644
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@@ -0,0 +1,37 @@
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+
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+##' identify node by interactive click
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+##'
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+##'
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+##' @rdname identify
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+##' @title identify
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+##' @param x tree view
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+##' @param ... additional parameters
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+##' @return node id
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+##' @importFrom grid convertX
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+##' @importFrom grid convertY
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+##' @importFrom grid pushViewport
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+##' @importFrom grid grid.locator
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+##' @importFrom grid unit
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+##' @importFrom grid dataViewport
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+##' @importFrom graphics identify
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+##' @method identify gg
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+##' @export
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+##' @author Guangchuang Yu
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+identify.gg <- function(x, ...) {
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+    tree_view <- x
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+    ## not used, since if x=NULL, it will call graphics::identify
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+    ## tree_view %<>% get_tree_view
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+
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+    x <- tree_view$data$x
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+    y <- tree_view$data$y
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+
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+    pushViewport(dataViewport(x, y))
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+    loc <- grid.locator('in') %>% as.numeric
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+
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+    xx <- as.numeric(convertX( unit(x,'native'), 'in' ))
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+    yy <- as.numeric(convertY( unit(y,'native'), 'in' ))
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+
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+    idx <- which.min( (xx-loc[1])^2 + (yy-loc[2])^2 )
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+    return(tree_view$data$node[idx])
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+}
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+