@@ -10,6 +10,7 @@ S3method(fortify,phylo4d)

 S3method(fortify,phyloseq)

 S3method(fortify,treedata)

 S3method(ggplot_add,facet_xlim)

+S3method(ggplot_add,scale_ggtree)

 S3method(groupClade,ggtree)

 S3method(groupOTU,ggtree)

 S3method(identify,gg)

@@ -186,6 +187,7 @@ importFrom(ggplot2,scale_x_reverse)

 importFrom(ggplot2,scale_y_continuous)

 importFrom(ggplot2,theme)

 importFrom(ggplot2,theme_bw)

+importFrom(ggplot2,waiver)

 importFrom(ggplot2,xlab)

 importFrom(ggplot2,xlim)

 importFrom(ggplot2,ylab)

@@ -1,5 +1,6 @@

 # ggtree 1.17.1

++ update `scale_x_ggtree`, now we can use `gheatmap() + scale_x_ggtree()` (2019-05-22, Wed)

 + extend `xlim_expand` to work with `ggplot2` (2019-05-20, Tue)

   - <https://yulab-smu.github.io/treedata-book/chapter9.html#xlim_expand>

 + add `legend_title` variable in `gheatmap` (2019-05-16, Thu)

@@ -84,58 +84,6 @@ get_heatmap_column_position <- function(treeview, by="bottom") {

     return(mapping)

 }

-##' scale x for tree with heatmap

-##'

-##'

-##' @title scale_x_ggtree

-##' @param tree_view tree view

-##' @param breaks breaks for tree

-##' @param labels lables for corresponding breaks

-##' @return tree view

-##' @importFrom ggplot2 scale_x_continuous

-##' @importFrom ggplot2 scale_x_date

-##' @export

-##' @author Guangchuang Yu

-scale_x_ggtree <- function(tree_view, breaks=NULL, labels=NULL) {

-    p <- get_tree_view(tree_view)

-

-    mrsd <- get("mrsd", envir=tree_view$plot_env)

-    if (!is.null(mrsd) && class(p$data$x) == "Date") {

-        x <- Date2decimal(p$data$x)

-    } else {

-        x <- p$data$x

-    }

-

-    if (is.null(breaks)) {

-        breaks <- graphics::hist(x, breaks=5, plot=FALSE)$breaks

-    }

-    m <- attr(p, "mapping")

-

-    if (!is.null(mrsd) &&class(m$to) == "Date") {

-        to <- Date2decimal(m$to)

-    } else {

-        to <- m$to

-    }

-

-    idx <- which(sapply(breaks, function(x) any(x > m$to)))

-    if (length(idx)) {

-        breaks <- breaks[-idx]

-    }

-

-    if (is.null(labels)) {

-        labels <- breaks

-    }

-

-    breaks <- c(breaks, to)

-    labels <- c(labels, gsub("\\.", "", as.character(m$from)))

-

-    if (!is.null(mrsd) && class(p$data$x) == "Date") {

-        p <- p + scale_x_date(breaks=decimal2Date(breaks), labels)

-    } else {

-        p <- p + scale_x_continuous(breaks=breaks, labels=labels)

-    }

-    return(p)

-}

new file mode 100644

@@ -0,0 +1,64 @@

+##' scale x for tree with gheatmap

+##'

+##'

+##' @title scale_x_ggtree

+##' @param breaks breaks for tree

+##' @param labels lables for corresponding breaks

+##' @return updated tree view

+##' @importFrom ggplot2 waiver

+##' @export

+##' @author Guangchuang Yu

+scale_x_ggtree <- function(breaks = waiver(), labels = waiver()) {

+    structure(list(breaks = breaks, labels = labels), class="scale_ggtree")

+}

+

+

+##' @importFrom ggplot2 scale_x_continuous

+##' @importFrom ggplot2 scale_x_date

+##' @method ggplot_add scale_ggtree

+##' @export

+ggplot_add.scale_ggtree <- function(object, plot, object_name) {

+    mrsd <- get("mrsd", envir = plot$plot_env)

+    if (!is.null(mrsd) && class(plot$data$x) == "Date") {

+        x <- Date2decimal(plot$data$x)

+    } else {

+        x <- plot$data$x

+    }

+

+    breaks <- object$breaks

+    labels <- object$labels

+

+    if (length(breaks) == 0) {

+        breaks <- graphics::hist(x, breaks=5, plot=FALSE)$breaks

+    }

+    m <- attr(plot, "mapping")

+

+    if (!is.null(mrsd) && class(m$to) == "Date") {

+        to <- Date2decimal(m$to)

+    } else {

+        to <- m$to

+    }

+    

+    idx <- which(sapply(breaks, function(x) any(x > m$to)))

+    if (length(idx)) {

+        breaks <- breaks[-idx]

+    }

+

+    if (length(labels) == 0) {

+        labels <- breaks

+    }

+

+    if (length(breaks) != length(labels)) {

+        stop("breaks and labels should be in equal length.")

+    }

+

+    breaks <- c(breaks, to)

+    labels <- c(labels, gsub("\\.", "", as.character(m$from)))

+

+    if (!is.null(mrsd) && class(plot$data$x) == "Date") {

+        obj <- scale_x_date(breaks=decimal2Date(breaks), labels)

+    } else {

+        obj <- scale_x_continuous(breaks=breaks, labels=labels)

+    }

+    ggplot_add(obj, plot, object_name)

+}

@@ -34,15 +34,23 @@ xlim_expand <- function(xlim, panel) {

 ##' @method ggplot_add facet_xlim

 ##' @export

 ggplot_add.facet_xlim <- function(object, plot, object_name) {

-    var <- quo_name(plot$facet$params$cols[[1]])

+    facet_col <- plot$facet$params$cols

+    var <- quo_name(facet_col[[1]])

+

     free_x <- plot$facet$params$free$x

-    if (!is.null(free_x) && !free_x) {

-        message('If you want to adjust xlim for specific panel, you need to set `scales = "free_x"`')

+    if (!is.null(free_x)) {

+        if (!free_x)

+            message('If you want to adjust xlim for specific panel, you need to set `scales = "free_x"`')

     }

+

     class(object) %<>% extract(., .!= "facet_xlim")

-    nm <- names(object$data)

-    nm[nm == '.panel']  <- var

-    names(object$data)  <- nm

+

+    if (!is.null(facet_col)) {

+        nm <- names(object$data)

+        nm[nm == '.panel']  <- var

+        names(object$data)  <- nm

+    }

+

     ggplot_add(object, plot, object_name)

 }

@@ -1,23 +1,21 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/experimental_function.R

+% Please edit documentation in R/scales.R

 \name{scale_x_ggtree}

 \alias{scale_x_ggtree}

 \title{scale_x_ggtree}

 \usage{

-scale_x_ggtree(tree_view, breaks = NULL, labels = NULL)

+scale_x_ggtree(breaks = waiver(), labels = waiver())

 }

 \arguments{

-\item{tree_view}{tree view}

-

 \item{breaks}{breaks for tree}

 \item{labels}{lables for corresponding breaks}

 }

 \value{

-tree view

+updated tree view

 }

 \description{

-scale x for tree with heatmap

+scale x for tree with gheatmap

 }

 \author{

 Guangchuang Yu