1. ggtree
  2. Commit 860448f433c721180e776c41bad3961d03d7129c
Browse code

add reference

Guangchuang Yu authored on 20/11/2019 03:58:34
Showing 7 changed files
R/facet_plot.R
History View file @ 860448f4
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@@ -20,6 +20,9 @@
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 ##' facet_plot(p, 'Trait', data = dd, geom=geom_point, mapping=aes(x=value))
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 ##' @export
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 ##' @author Guangchuang Yu
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+##' @references G Yu, TTY Lam, H Zhu, Y Guan (2018). Two methods for mapping and visualizing associated data
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+##' on phylogeny using ggtree. Molecular Biology and Evolution, 35(2):3041-3043.
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+##' <https://doi.org/10.1093/molbev/msy194>
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 facet_plot <- function(p, mapping=NULL, data, geom, panel, ...) {
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     p + geom_facet(panel = panel, data = data,
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                    geom = geom, mapping = mapping, ...)
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@@ -44,6 +47,9 @@ geom_facet <- function(mapping=NULL, data, geom, panel, ...) {
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 ##' @return data frame or a list of data frames
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 ##' @export
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 ##' @author Guangchuang Yu
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+##' @references G Yu, TTY Lam, H Zhu, Y Guan (2018). Two methods for mapping and visualizing associated data
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+##' on phylogeny using ggtree. Molecular Biology and Evolution, 35(2):3041-3043.
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+##' <https://doi.org/10.1093/molbev/msy194>
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 facet_data <- function(tree_view, panel) {
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     n <- length(tree_view$layers)
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     j <- which(vapply(1:n, function(i) {
R/ggtree.R
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@@ -27,8 +27,16 @@
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 ##' @export
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 ##' @author Yu Guangchuang
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 ##' @seealso [ape::ladderize()]
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+##' @references 1. G Yu, TTY Lam, H Zhu, Y Guan (2018). Two methods for mapping and visualizing associated data
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+##' on phylogeny using ggtree. Molecular Biology and Evolution, 35(2):3041-3043.
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+##' <https://doi.org/10.1093/molbev/msy194>
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+##'
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+##' 2. G Yu, DK Smith, H Zhu, Y Guan, TTY Lam (2017). ggtree: an R package for
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+##' visualization and annotation of phylogenetic trees with their covariates and
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+##' other associated data. Methods in Ecology and Evolution, 8(1):28-36.
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+##' <https://doi.org/10.1111/2041-210X.12628>
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 ##' @examples
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-##' require(ape)
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+##' require(ape)
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 ##' tr <- rtree(10)
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 ##' ggtree(tr)
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 ggtree <- function(tr,
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@@ -87,13 +95,15 @@ ggtree <- function(tr,
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     p <- p + geom_tree(layout=layout, multiPhylo=multiPhylo, ...)
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-    p <- p + theme_tree() +
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-        scale_y_continuous(expand = expand_scale(0, 0.6))
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+    p <- p + theme_tree()
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     if (layout == "circular" || layout == "radial") {
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         p <- p + layout_circular()
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     } else if (layout == "fan") {
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         p <- p + layout_fan(open.angle)
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+    } else {
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+        p <- p +
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+            scale_y_continuous(expand = expand_scale(0, 0.6))
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     }
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     class(p) <- c("ggtree", class(p))
R/operator.R
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@@ -40,6 +40,9 @@
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 ##'              value=round(abs(rnorm(13, mean=70, sd=10)), digits=1))
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 ##' row.names(dd) <- NULL
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 ##' p %<+% dd + geom_text(aes(color=place, label=label), hjust=-0.5)
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+##' @references G Yu, TTY Lam, H Zhu, Y Guan (2018). Two methods for mapping and visualizing associated data
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+##' on phylogeny using ggtree. Molecular Biology and Evolution, 35(2):3041-3043.
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+##' <https://doi.org/10.1093/molbev/msy194>
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 `%<+%` <- function(pg, data) {
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     if (! is.data.frame(data)) {
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         stop("input should be a data.frame...")
man/add-TREEDATA.Rd
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@@ -27,6 +27,11 @@ dd <- data.frame(taxa=LETTERS[1:13],
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 row.names(dd) <- NULL
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 p \%<+\% dd + geom_text(aes(color=place, label=label), hjust=-0.5)
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 }
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+\references{
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+G Yu, TTY Lam, H Zhu, Y Guan (2018). Two methods for mapping and visualizing associated data
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+on phylogeny using ggtree. Molecular Biology and Evolution, 35(2):3041-3043.
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+\url{https://doi.org/10.1093/molbev/msy194}
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+}
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 \author{
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 Guangchuang Yu
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 }
man/facet-plot.Rd
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@@ -39,6 +39,11 @@ dd = data.frame(id=tr$tip.label, value=abs(rnorm(10)))
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 p <- ggtree(tr)
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 facet_plot(p, 'Trait', data = dd, geom=geom_point, mapping=aes(x=value))
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 }
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+\references{
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+G Yu, TTY Lam, H Zhu, Y Guan (2018). Two methods for mapping and visualizing associated data
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+on phylogeny using ggtree. Molecular Biology and Evolution, 35(2):3041-3043.
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+\url{https://doi.org/10.1093/molbev/msy194}
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+}
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 \author{
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 Guangchuang Yu
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 }
man/facet_data.Rd
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@@ -17,6 +17,11 @@ data frame or a list of data frames
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 \description{
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 extract data used in \code{facet_plot} or \code{geom_facet}
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 }
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+\references{
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+G Yu, TTY Lam, H Zhu, Y Guan (2018). Two methods for mapping and visualizing associated data
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+on phylogeny using ggtree. Molecular Biology and Evolution, 35(2):3041-3043.
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+\url{https://doi.org/10.1093/molbev/msy194}
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+}
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 \author{
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 Guangchuang Yu
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 }
man/ggtree.Rd
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@@ -54,10 +54,21 @@ Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628
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 drawing phylogenetic tree from phylo object
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 }
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 \examples{
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-require(ape)
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+require(ape)
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 tr <- rtree(10)
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 ggtree(tr)
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 }
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+\references{
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+\enumerate{
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+\item G Yu, TTY Lam, H Zhu, Y Guan (2018). Two methods for mapping and visualizing associated data
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+on phylogeny using ggtree. Molecular Biology and Evolution, 35(2):3041-3043.
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+\url{https://doi.org/10.1093/molbev/msy194}
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+\item G Yu, DK Smith, H Zhu, Y Guan, TTY Lam (2017). ggtree: an R package for
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+visualization and annotation of phylogenetic trees with their covariates and
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+other associated data. Methods in Ecology and Evolution, 8(1):28-36.
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+\url{https://doi.org/10.1111/2041-210X.12628}
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+}
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+}
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 \seealso{
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 \code{\link[ape:ladderize]{ape::ladderize()}}
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 }