@@ -54,3 +54,4 @@ Packaged: 2014-12-03 08:16:14 UTC; root

 biocViews: Alignment, Annotation, Clustering, DataImport,

     MultipleSequenceAlignment, ReproducibleResearch, Software, Visualization

 RoxygenNote: 6.1.1

+Roxygen: list(markdown = TRUE)

@@ -16,7 +16,7 @@ S3method(fortify,phylog)

 S3method(fortify,phyloseq)

 S3method(fortify,treedata)

 S3method(fortify,twins)

-S3method(ggplot_add,align_axis)

+S3method(ggplot_add,axisAlign)

 S3method(ggplot_add,cladelabel)

 S3method(ggplot_add,facet_plot)

 S3method(ggplot_add,facet_xlim)

@@ -45,8 +45,6 @@ export(StatBalance)

 export(StatHilight)

 export(add_colorbar)

 export(aes)

-export(align_x)

-export(align_y)

 export(annotation_image)

 export(arrow)

 export(as.polytomy)

@@ -135,8 +133,10 @@ export(theme_tree2)

 export(unit)

 export(viewClade)

 export(xlim)

+export(xlim_align)

 export(xlim_expand)

 export(xlim_tree)

+export(ylim_align)

 exportMethods(gzoom)

 exportMethods(scale_color)

 importFrom(ape,di2multi)

@@ -1,7 +1,9 @@

 # ggtree 2.1.1

-+ `align_x` and `align_y` for setting x or y limits of a ggplot based on another ggplot object (2019-10-31, Thu)

++ convert roxygen documents using markdown (2019-11-01, Fri)

++ `xlim_align` and `ylim_align` to uniformize axis limits of ggplot objects (2019-10-31, Thu)

   - <https://yulab-smu.github.io/treedata-book/chapter7.html#composite_plot>

+  - <https://yulab-smu.github.io/treedata-book/docs/chapter10.html#axis_align>

 + fixed `fontface` warning message when `align=TRUE` in `geom_tiplab` (2019-10-30, Wed)

   - <https://github.com/YuLab-SMU/ggtree/issues/260>

@@ -5,7 +5,7 @@ setOldClass("ggtree")

 ##' @name scale_color

 ##' @rdname scale_color-methods

 ##' @title scale_color method

-##' @param object \code{treedata} object

+##' @param object `treedata` object

 ##' @param by one of numerical attributes

 ##' @param ... additional parameter

 ##' @return color vector

@@ -58,29 +58,51 @@ revts <- function(treeview) {

-##' set axis limits (x or y specific by 'by' parameter) of a ggplot object (left hand side)

-##' based on the x (align_x function) or y (align_y function) limits of another ggplot object (right hand side).

-##' This is useful for using cowplot or patchwork to align ggplot objects.

+##' set axis limits (x or y) of a `ggplot` object (left hand side of `+`)

+##' based on the x (`xlim_align`) or y (`ylim_align`) limits of another `ggplot` object (right hand side of `+`).

+##' This is useful for using `cowplot` or `patchwork` to align `ggplot` objects.

 ##'

 ##'

-##' @title align_x

+##' @title xlim_align

 ##' @rdname align_axis

 ##' @param gg ggplot object

-##' @param expand_limits amount to expand the limits

-##' @param by one of 'x' or 'y'

-##' @return ggplot2 object with new limits and expand

-##' @importFrom ggplot2 expand_scale

+##' @param limits vector of limits. If NULL, determine from `gg`. 

+##' @return ggplot2 object with new limits

 ##' @export

 ##' @author Guangchuang Yu

-align_x <- function(gg, expand_limits = expand_scale(0, 0.6), by = 'x') {

-    structure(list(gg = gg, expand_limits = expand_limits, by = by, axis = "x"),

-              class = "align_axis")

+xlim_align <- function(gg, limits = NULL) {

+    axis_align(gg = gg, limits = limits, axis = 'x')

 }

 ##' @rdname align_axis

-##' @title align_y

+##' @title ylim_align

 ##' @export

-align_y <- function(gg, expand_limits = expand_scale(0, 0.6), by = 'y') { 

-    structure(list(gg = gg, expand_limits = expand_limits, by = by, axis = "y"),

-              class = "align_axis")

+ylim_align <- function(gg, limits = NULL) {

+    axis_align(gg = gg, limits = limits, axis = 'y')

 }

+

+axis_align <- function(gg, limits = NULL, axis) {

+    if (is.null(limits)) {

+        if (axis == "x") {

+            limits <- xrange(gg)

+        } else {

+            limits <- yrange(gg)

+        }

+    }

+    structure(list(limits = limits, axis = axis),

+              class = "axisAlign")

+}

+

+

+yrange <- function(gg) {

+    ggrange(gg, "y.range")

+}

+

+xrange <- function(gg) {

+    ggrange(gg, "x.range")

+}

+

+ggrange <- function(gg, var) {

+    ggplot_build(gg)$layout$panel_params[[1]][[var]]

+}

+

@@ -42,7 +42,7 @@ viewClade <- function(tree_view=NULL, node, xmax_adjust=0) {

     ## xd <- tree_view$data$branch.length[node]/2

     cpos <- get_clade_position(tree_view, node=node)

-    xmax <- ggplot_build(tree_view)$layout$panel_params[[1]]$x.range[2]

+    xmax <- xrange(tree_view)[2]

     attr(tree_view, 'viewClade') <- TRUE

     attr(tree_view, 'viewClade_node') <- node

@@ -51,8 +51,8 @@ phylopic <- function(tree_view, phylopic_id,

 ##' @param subview a ggplot or grob object

 ##' @param x x position

 ##' @param y y position

-##' @param width width of subview, [0,1]

-##' @param height height of subview, [0,1]

+##' @param width width of subview

+##' @param height height of subview

 ##' @return ggplot object

 ##' @importFrom ggplot2 annotation_custom

 ##' @importFrom ggplot2 ggplotGrob

@@ -122,7 +122,7 @@ gzoom.ggtree <- function(tree_view, focus, widths=c(.3, .7), xmax_adjust=0) {

 ##' @title gzoom method

 ##' @rdname gzoom-methods

 ##' @exportMethod gzoom

-##' @param xmax_adjust adjust xmax (xlim[2])

+##' @param xmax_adjust adjust xmax (`xlim[2]`)

 ##' @aliases gzoom,ggtree-method

 setMethod("gzoom", signature(object="ggtree"),

           function(object, focus, widths=c(.3, .7), xmax_adjust=0) {

@@ -4,7 +4,7 @@

 ##' @title range_format

 ##' @param x input list

 ##' @param trans transformation function

-##' @return character vector of '[lower, upper]'

+##' @return character vector of `[lower, upper]`

 ##' @export

 ##' @author Guangchuang Yu

 range_format <- function(x, trans = NULL) {

@@ -16,8 +16,8 @@

 #' @importFrom ggplot2 GeomRect

 #' @importFrom utils packageVersion

 #' @author Justin Silverman and modified by Guangchuang Yu

-#' @references J. Silverman, et al. \emph{A phylogenetic transform enhances

-#'   analysis of compositional microbiota data}. (in preparation)

+#' @references J. Silverman, et al. *A phylogenetic transform enhances

+#'   analysis of compositional microbiota data*. (in preparation)

 geom_balance <- function(node, fill="steelblue", color='white', alpha=.5, extend=0, extendto=NULL) {

   data = NULL

@@ -21,7 +21,7 @@

 ##' @return ggplot layers

 ##' @export

 ##' @author Guangchuang Yu

-##' @seealso \link{geom_cladelabel2}

+##' @seealso [geom_cladelabel2]

 geom_cladelabel <- function(node, label,

                             offset      = 0,

                             offset.text = 0,

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

 ##' @return ggplot layers

 ##' @export

 ##' @author JustGitting

-##' @seealso \link{geom_cladelabel}

+##' @seealso [geom_cladelabel]

 geom_cladelabel2 <- function(node, label, offset=0, offset.text=0, offset.bar=0,

                             align=FALSE, barsize=0.5, fontsize=3.88, hjust = 0,

                             geom="text",

@@ -23,7 +23,7 @@

 ##' @importFrom ggplot2 position_nudge

 ##' @export

 ##' @seealso

-##' \link[ggplot2]{geom_label}

+##' [geom_label][ggplot2::geom_label]

 ##' @author Guangchuang Yu

 geom_label2 <- function(mapping = NULL, data = NULL,

                         ...,

@@ -105,7 +105,7 @@ geom_rootpoint <- function(mapping = NULL, data = NULL,

 ##' @importFrom ggplot2 layer

 ##' @export

 ##' @seealso

-##' \link[ggplot2]{geom_point}

+##' [geom_point][ggplot2::geom_point]

 ##' @return point layer

 ##' @author Guangchuang Yu

 geom_point2 <- function(mapping = NULL, data = NULL, stat = "identity",

@@ -42,7 +42,7 @@ geom_aline <- function(mapping=NULL, linetype="dotted", size=1, ...) {

 ##' @importFrom ggplot2 layer

 ##' @export

 ##' @seealso

-##' \link[ggplot2]{geom_segment}

+##' [geom_segment][ggplot2::geom_segment]

 ##' @return add segment layer

 ##' @author Guangchuang Yu

 geom_segment2 <- function(mapping = NULL, data = NULL, stat = "identity",

@@ -23,7 +23,7 @@

 ##' @importFrom rvcheck get_aes_var

 ##' @export

 ##' @seealso

-##' \link[ggplot2]{geom_text}

+##' [geom_text][ggplot2::geom_text]

 ##' @author Guangchuang Yu

 geom_text2 <- function(mapping = NULL, data = NULL,

                        ...,

@@ -95,8 +95,8 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE, lin

 ##' @return tip label layer

 ##' @export

 ##' @author Guangchuang Yu

-##' @references \url{https://groups.google.com/forum/#!topic/bioc-ggtree/o35PV3iHO-0}

-##' @seealso \link{geom_tiplab}

+##' @references <https://groups.google.com/forum/#!topic/bioc-ggtree/o35PV3iHO-0>

+##' @seealso [geom_tiplab]

 geom_tiplab2 <- function(mapping=NULL, hjust=0, ...) {

     angle <- isTip <- node <- NULL

     m1 <- aes(subset=(isTip & (angle < 90 | angle > 270)), angle=angle, node = node)

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

 ##' visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics

-##' \code{ggtree} provides functions for visualizing phylogenetic tree and its associated data in R.

+##' `ggtree` provides functions for visualizing phylogenetic tree and its associated data in R.

 ##'

 ##' If you use ggtree in published research, please cite:

 ##' Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.

@@ -9,10 +9,10 @@

 ##' @param as.Date logical whether using Date class in time tree

 ##' @param yscale y scale

 ##' @param yscale_mapping yscale mapping for category variable

-##' @param ladderize logical (default \code{TRUE}). Should the tree be re-organized to have a 'ladder'

+##' @param ladderize logical (default `TRUE`). Should the tree be re-organized to have a 'ladder'

 ##' aspect?

-##' @param right logical. If \code{ladderize = TRUE}, should the ladder have the smallest clade on the

-##' right-hand side? See \code{\link[ape]{ladderize}} for more information. 

+##' @param right logical. If `ladderize = TRUE`, should the ladder have the smallest clade on the

+##' right-hand side? See [ape::ladderize()] for more information. 

 ##' @param branch.length variable for scaling branch, if 'none' draw cladogram

 ##' @param root.position position of the root node (default = 0)

 ##' @return tree

@@ -26,7 +26,7 @@

 ##' @importFrom ggplot2 coord_polar

 ##' @export

 ##' @author Yu Guangchuang

-##' @seealso \code{\link[ape]{ladderize}}

+##' @seealso [ape::ladderize()]

 ##' @examples

 ##' require(ape)

 ##' tr <- rtree(10)

@@ -21,49 +21,46 @@ ggplot_add.facet_xlim <- function(object, plot, object_name) {

 }

-##' @method ggplot_add align_axis

+##' @method ggplot_add axisAlign

 ##' @export

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

-    gg <- object$gg

-    v <- get_aes_var(gg$mapping, object$axis)

-    limits <- range(gg$data[[v]])

-

-    expand_limits <- object$expand_limits

-    limits[1] <- limits[1] + (limits[1] * expand_limits[1]) - expand_limits[2]

-    limits[2] <- limits[2] + (limits[2] * expand_limits[3]) + expand_limits[4]

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

+    limits <- object$limits

+    ## expand_limits <- object$expand_limits

+    ## limits[1] <- limits[1] + (limits[1] * expand_limits[1]) - expand_limits[2]

+    ## limits[2] <- limits[2] + (limits[2] * expand_limits[3]) + expand_limits[4]

     if (object$axis == 'x') {

-        if (object$by == "x") {

-            if (is(plot$coordinates, "CoordFlip")) {

-                message("the plot was flipped and the x limits will be applied to y-axis")

-                scale_lim <- scale_y_continuous(limits = limits, expand = c(0, 0))

-            } else {

-                scale_lim <- scale_x_continuous(limits = limits, expand = c(0, 0))

-            }

+        ## if (object$by == "x") {

+        if (is(plot$coordinates, "CoordFlip")) {

+            message("the plot was flipped and the x limits will be applied to y-axis")

+            scale_lim <- scale_y_continuous(limits = limits, expand = c(0, 0))

         } else {

-            if (is(plot$coordinates, "CoordFlip")) {

-                message("the plot was flipped and the x limits will be applied to x-axis")

-                scale_lim <- scale_x_continuous(limits=limits, expand=c(0,0))

-            } else {

-                scale_lim <- scale_y_continuous(limits=limits, expand=c(0,0))

-            }

+            scale_lim <- scale_x_continuous(limits = limits, expand = c(0, 0))

         }

+        ## } else {

+        ##     if (is(plot$coordinates, "CoordFlip")) {

+        ##         message("the plot was flipped and the x limits will be applied to x-axis")

+        ##         scale_lim <- scale_x_continuous(limits=limits, expand=c(0,0))

+        ##     } else {

+        ##         scale_lim <- scale_y_continuous(limits=limits, expand=c(0,0))

+        ##     }

+        ## }

     } else { ## axis == 'y'

-        if (object$by == "x") {

-            if (is(plot$coordinates, "CoordFlip")) {

-                message("the plot was flipped and the y limits will be applied to y-axis")

-                scale_lim <- scale_y_continuous(limits = limits, expand = c(0, 0))

-            } else {

-                scale_lim <- scale_x_continuous(limits = limits, expand = c(0, 0))

-            }

+        ## if (object$by == "x") {

+        ##     if (is(plot$coordinates, "CoordFlip")) {

+        ##         message("the plot was flipped and the y limits will be applied to y-axis")

+        ##         scale_lim <- scale_y_continuous(limits = limits, expand = c(0, 0))

+        ##     } else {

+        ##         scale_lim <- scale_x_continuous(limits = limits, expand = c(0, 0))

+        ##     }

+        ## } else {

+        if (is(plot$coordinates, "CoordFlip")) {

+            message("the plot was flipped and the y limits will be applied to x-axis")

+            scale_lim <- scale_x_continuous(limits=limits, expand=c(0,0))

         } else {

-            if (is(plot$coordinates, "CoordFlip")) {

-                message("the plot was flipped and the y limits will be applied to x-axis")

-                scale_lim <- scale_x_continuous(limits=limits, expand=c(0,0))

-            } else {

-                scale_lim <- scale_y_continuous(limits=limits, expand=c(0,0))

-            }

+            scale_lim <- scale_y_continuous(limits=limits, expand=c(0,0))

         }

+        ## }

     }

     ggplot_add(scale_lim, plot, object_name)

 }

@@ -78,6 +75,7 @@ ggplot_add.geom_range <- function(object, plot, object_name) {

 }

 ##' @method ggplot_add layout_ggtree

+##' @importFrom ggplot2 expand_scale

 ##' @export

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

     if(object$layout == 'fan') {

@@ -290,13 +290,13 @@ applyLayoutDaylight <- function(df, node_id){

 ##' Find the right (clockwise rotation, angle from +ve x-axis to furthest subtree nodes) and

-##' left (anti-clockwise angle from +ve x-axis to subtree) Returning arc angle in [0, 2] (0 to 360) domain.

+##' left (anti-clockwise angle from +ve x-axis to subtree) Returning arc angle in `[0, 2]` (0 to 360) domain.

 ##'

 ##' @title getTreeArcAngles

 ##' @param df tree data.frame

 ##' @param origin_id node id from which to calculate left and right hand angles of subtree.

 ##' @param subtree named list of root id of subtree (node) and list of node ids for given subtree (subtree).

-##' @return named list with right and left angles in range [0,2] i.e 1 = 180 degrees, 1.5 = 270 degrees.

+##' @return named list with right and left angles in range `[0,2]` i.e 1 = 180 degrees, 1.5 = 270 degrees.

 getTreeArcAngles <- function(df, origin_id, subtree) {

     df_x = df$x

     df_y = df$y

@@ -437,11 +437,12 @@ getTreeArcAngles <- function(df, origin_id, subtree) {

 ##' Rotate the points in a tree data.frame around a pivot node by the angle specified.

 ##'

-##' @title rotateTreePoints.data.fram

+##' @title rotateTreePoints.data.frame

+##' @rdname rotateTreePoints

 ##' @param df tree data.frame

 ##' @param pivot_node is the id of the pivot node.

 ##' @param nodes list of node numbers that are to be rotated by angle around the pivot_node

-##' @param angle in range [0,2], ie degrees/180, radians/pi

+##' @param angle in range `[0,2]`, ie degrees/180, radians/pi

 ##' @return updated tree data.frame with points rotated by angle

 rotateTreePoints.df <- function(df, pivot_node, nodes, angle){

   # Rotate nodes around pivot_node.

@@ -477,7 +478,7 @@ rotateTreePoints.df <- function(df, pivot_node, nodes, angle){

 ##' @param df tree data.frame

 ##' @param origin_node_id origin node id number

 ##' @param node_id end node id number

-##' @return angle in range [-1, 1], i.e. degrees/180, radians/pi

+##' @return angle in range `[-1, 1]`, i.e. degrees/180, radians/pi

 getNodeAngle.df <- function(df, origin_node_id, node_id){

   if (origin_node_id != node_id) {

     df_x = df$x

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

-

 ##' @importFrom ggplot2 last_plot

 get_tree_view <- function(tree_view) {

     if (is.null(tree_view))

@@ -1,28 +1,26 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/x-axis.R

-\name{align_x}

-\alias{align_x}

-\alias{align_y}

-\title{align_x}

+% Please edit documentation in R/axis.R

+\name{xlim_align}

+\alias{xlim_align}

+\alias{ylim_align}

+\title{xlim_align}

 \usage{

-align_x(gg, expand_limits = expand_scale(0, 0.6), by = "x")

+xlim_align(gg, limits = NULL)

-align_y(gg, expand_limits = expand_scale(0, 0.6), by = "y")

+ylim_align(gg, limits = NULL)

 }

 \arguments{

 \item{gg}{ggplot object}

-\item{expand_limits}{amount to expand the limits}

-

-\item{by}{one of 'x' or 'y'}

+\item{limits}{vector of limits. If NULL, determine from \code{gg}.}

 }

 \value{

-ggplot2 object with new limits and expand

+ggplot2 object with new limits

 }

 \description{

-set axis limits (x or y specific by 'by' parameter) of a ggplot object (left hand side)

-based on the x (align_x function) or y (align_y function) limits of another ggplot object (right hand side).

-This is useful for using cowplot or patchwork to align ggplot objects.

+set axis limits (x or y) of a \code{ggplot} object (left hand side of \code{+})

+based on the x (\code{xlim_align}) or y (\code{ylim_align}) limits of another \code{ggplot} object (right hand side of \code{+}).

+This is useful for using \code{cowplot} or \code{patchwork} to align \code{ggplot} objects.

 }

 \author{

 Guangchuang Yu

@@ -15,7 +15,7 @@ facet_data(tree_view, panel)

 data frame or a list of data frames

 }

 \description{

-extract data used in `facet_plot` or `geom_facet`

+extract data used in \code{facet_plot} or \code{geom_facet}

 }

 \author{

 Guangchuang Yu

@@ -32,7 +32,7 @@ correspond to multichotomies will not be displayed.

 }

 \references{

 J. Silverman, et al. \emph{A phylogenetic transform enhances

-  analysis of compositional microbiota data}. (in preparation)

+analysis of compositional microbiota data}. (in preparation)

 }

 \author{

 Justin Silverman and modified by Guangchuang Yu

@@ -49,7 +49,7 @@ label layer

 geom_label2 support aes(subset) via setup_data

 }

 \seealso{

-\link[ggplot2]{geom_label}

+\link[ggplot2:geom_label]{geom_label}

 }

 \author{

 Guangchuang Yu

@@ -11,7 +11,7 @@ geom_motif(mapping, data, on, label, align = "centre", ...)

 \item{data}{data}

-\item{on}{gene to center (i.e. set middle position of the `on` gene to 0)}

+\item{on}{gene to center (i.e. set middle position of the \code{on} gene to 0)}

 \item{label}{specify a column to be used to label genes}

@@ -32,7 +32,7 @@ point layer

 geom_point2 support aes(subset) via setup_data

 }

 \seealso{

-\link[ggplot2]{geom_point}

+\link[ggplot2:geom_point]{geom_point}

 }

 \author{

 Guangchuang Yu

@@ -30,7 +30,7 @@ geom_segment2(mapping = NULL, data = NULL, stat = "identity",

 \item{arrow}{specification for arrow heads, as created by arrow().}

-\item{arrow.fill}{fill color to usse for the arrow head (if closed). `NULL` means use `colour` aesthetic.}

+\item{arrow.fill}{fill color to usse for the arrow head (if closed). \code{NULL} means use \code{colour} aesthetic.}

 \item{...}{additional parameter}

 }

@@ -41,7 +41,7 @@ add segment layer

 geom_segment2 support aes(subset) via setup_data

 }

 \seealso{

-\link[ggplot2]{geom_segment}

+\link[ggplot2:geom_segment]{geom_segment}

 }

 \author{

 Guangchuang Yu

@@ -18,7 +18,7 @@ positive values produce right-hand curves, and zero produces a straight line.}

 \item{arrow}{specification for arrow heads, as created by arrow().}

-\item{arrow.fill}{fill color to usse for the arrow head (if closed). `NULL` means use `colour` aesthetic.}

+\item{arrow.fill}{fill color to usse for the arrow head (if closed). \code{NULL} means use \code{colour} aesthetic.}

 \item{...}{additional parameter}

 }

@@ -44,7 +44,7 @@ text layer

 geom_text2 support aes(subset) via setup_data

 }

 \seealso{

-\link[ggplot2]{geom_text}

+\link[ggplot2:geom_text]{geom_text}

 }

 \author{

 Guangchuang Yu

@@ -14,7 +14,7 @@ getNodeAngle.df(df, origin_node_id, node_id)

 \item{node_id}{end node id number}

 }

 \value{

-angle in range [-1, 1], i.e. degrees/180, radians/pi

+angle in range \code{[-1, 1]}, i.e. degrees/180, radians/pi

 }

 \description{

 Get the angle between the two nodes specified.

@@ -14,9 +14,9 @@ getTreeArcAngles(df, origin_id, subtree)

 \item{subtree}{named list of root id of subtree (node) and list of node ids for given subtree (subtree).}

 }

 \value{

-named list with right and left angles in range [0,2] i.e 1 = 180 degrees, 1.5 = 270 degrees.

+named list with right and left angles in range \code{[0,2]} i.e 1 = 180 degrees, 1.5 = 270 degrees.

 }

 \description{

 Find the right (clockwise rotation, angle from +ve x-axis to furthest subtree nodes) and

-left (anti-clockwise angle from +ve x-axis to subtree) Returning arc angle in [0, 2] (0 to 360) domain.

+left (anti-clockwise angle from +ve x-axis to subtree) Returning arc angle in \code{[0, 2]} (0 to 360) domain.

 }

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

 get_heatmap_column_position(treeview, by = "bottom")

 }

 \arguments{

-\item{treeview}{output of `gheatmap`}

+\item{treeview}{output of \code{gheatmap}}

 \item{by}{one of 'bottom' or 'top'}

 }

@@ -16,7 +16,7 @@ data.frame

 }

 \description{

 return a data.frame that contains position information

-for labeling column names of heatmap produced by `gheatmap` function

+for labeling column names of heatmap produced by \code{gheatmap} function

 }

 \author{

 Guangchuang Yu

@@ -34,7 +34,7 @@ ggtree(tr, mapping = NULL, layout = "rectangular", open.angle = 0,

 aspect?}

 \item{right}{logical. If \code{ladderize = TRUE}, should the ladder have the smallest clade on the

-right-hand side? See \code{\link[ape]{ladderize}} for more information.}

+right-hand side? See \code{\link[ape:ladderize]{ape::ladderize()}} for more information.}

 \item{branch.length}{variable for scaling branch, if 'none' draw cladogram}

@@ -59,7 +59,7 @@ tr <- rtree(10)

 ggtree(tr)

 }

 \seealso{

-\code{\link[ape]{ladderize}}

+\code{\link[ape:ladderize]{ape::ladderize()}}

 }

 \author{

 Yu Guangchuang

@@ -30,7 +30,7 @@ gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...)

 \item{...}{additional parameter}

-\item{xmax_adjust}{adjust xmax (xlim[2])}

+\item{xmax_adjust}{adjust xmax (\code{xlim[2]})}

 }

 \value{

 figure

@@ -21,15 +21,12 @@ tree as data.frame with equal angle layout.

 }

 \references{

 The following aglorithm aims to implement the vague description of the "Equal-daylight Algorithm"

-in "Inferring Phylogenies" pp 582-584 by Joseph Felsenstein.

-

-```

-Leafs are subtrees with no children

+in "Inferring Phylogenies" pp 582-584 by Joseph Felsenstein.\preformatted{Leafs are subtrees with no children

 Initialise tree using equal angle algorithm

 tree_df = equal_angle(tree)

 nodes = get list of nodes in tree_df breadth-first

 nodes = remove tip nodes.

-```

+}

 }

@@ -12,7 +12,7 @@ range_format(x, trans = NULL)

 \item{trans}{transformation function}

 }

 \value{

-character vector of '[lower, upper]'

+character vector of \code{[lower, upper]}

 }

 \description{

 format a list of range (HPD, CI, etc that has length of 2)

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

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/x-axis.R

+% Please edit documentation in R/axis.R

 \name{revts}

 \alias{revts}

 \title{revts}

similarity index 84%

rename from man/rotateTreePoints.df.Rd

rename to man/rotateTreePoints.Rd

@@ -2,7 +2,7 @@

 % Please edit documentation in R/tree-utilities.R

 \name{rotateTreePoints.df}

 \alias{rotateTreePoints.df}

-\title{rotateTreePoints.data.fram}

+\title{rotateTreePoints.data.frame}

 \usage{

 rotateTreePoints.df(df, pivot_node, nodes, angle)

 }

@@ -13,7 +13,7 @@ rotateTreePoints.df(df, pivot_node, nodes, angle)

 \item{nodes}{list of node numbers that are to be rotated by angle around the pivot_node}

-\item{angle}{in range [0,2], ie degrees/180, radians/pi}

+\item{angle}{in range \code{[0,2]}, ie degrees/180, radians/pi}

 }

 \value{

 updated tree data.frame with points rotated by angle

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

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/x-axis.R

+% Please edit documentation in R/axis.R

 \name{scale_x_range}

 \alias{scale_x_range}

 \title{scale_x_range}

@@ -15,9 +15,9 @@ subview(mainview, subview, x, y, width = 0.1, height = 0.1)

 \item{y}{y position}

-\item{width}{width of subview, [0,1]}

+\item{width}{width of subview}

-\item{height}{height of subview, [0,1]}

+\item{height}{height of subview}

 }

 \value{

 ggplot object

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

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/x-axis.R

+% Please edit documentation in R/axis.R

 \name{xlim_expand}

 \alias{xlim_expand}

 \title{xlim_expand}

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

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/x-axis.R

+% Please edit documentation in R/axis.R

 \name{xlim_tree}

 \alias{xlim_tree}

 \title{xlim_tree}