Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add "daylight" layout method for unrooted trees. #124

Merged
merged 3 commits into from
Apr 10, 2017
Merged

Add "daylight" layout method for unrooted trees. #124

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
40f0f07
Added layout.method parameter to ggtree.R to modify behaviour of layo…
Apr 6, 2017
d86c9a9
gitignore and Rbuildignore have been updated by RStudio. It was not m…
Apr 6, 2017
fb2b245
Pull from fork of ggtree.
Apr 6, 2017
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 5 additions & 0 deletions .Rbuildignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,4 +11,9 @@ mkdocs
docs
logo.png.github
.github
<<<<<<< HEAD
^.*\.Rproj$
^\.Rproj\.user$
=======
ggtree_sticker.R
>>>>>>> 6c3d0a213ebba123a58af768ef6d7b4ec93b85d1
3 changes: 3 additions & 0 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,3 +8,6 @@ __init__.py
__pycache__
__init__.pyc

.Rproj.user
ggtree.Rproj
.RData
11 changes: 9 additions & 2 deletions R/ggtree.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
##' @param tr phylo object
##' @param mapping aes mapping
##' @param layout one of 'rectangular', 'slanted', 'fan', 'circular', 'radial' or 'unrooted'
##' @param layout.method of 'equal_angle', 'daylight'.
##' @param open.angle open angle, only for 'fan' layout
##' @param mrsd most recent sampling date
##' @param as.Date logical whether using Date class in time tree
Expand Down Expand Up @@ -33,6 +34,7 @@
ggtree <- function(tr,
mapping = NULL,
layout = "rectangular",
layout.method = "equal_angle",
open.angle = 0,
mrsd = NULL,
as.Date = FALSE,
Expand All @@ -44,8 +46,10 @@ ggtree <- function(tr,
ndigits = NULL,
...) {

# Check if layout string is valid.
layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular", "radial", "unrooted"))

layout.method %<>% match.arg(c("equal_angle", "daylight"))

if (is(tr, "r8s") && branch.length == "branch.length") {
branch.length = "TREE"
}
Expand All @@ -60,8 +64,11 @@ ggtree <- function(tr,
} else {
mapping <- modifyList(aes_(~x, ~y), mapping)
}
p <- ggplot(tr, mapping=mapping,

p <- ggplot(tr,
mapping = mapping,
layout = layout,
layout.method = layout.method,
mrsd = mrsd,
as.Date = as.Date,
yscale = yscale,
Expand Down
75 changes: 55 additions & 20 deletions R/method-fortify.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -110,6 +110,7 @@ rm.singleton.newick <- function(nwk, outfile = NULL) {
##' @export
fortify.beast <- function(model, data,
layout = "rectangular",
layout.method = "equal_angle",
yscale = "none",
ladderize = TRUE,
right = FALSE,
Expand All @@ -119,7 +120,8 @@ fortify.beast <- function(model, data,

model <- set_branch_length(model, branch.length)
phylo <- model@phylo
df <- fortify(phylo, layout=layout, branch.length=branch.length,
df <- fortify(phylo, layout=layout, layout.method=layout.method,
branch.length=branch.length,
ladderize=ladderize, right=right, mrsd = mrsd, ...)

stats <- model@stats
Expand Down Expand Up @@ -220,6 +222,7 @@ fortify.beast <- function(model, data,
##' @export
fortify.codeml <- function(model, data,
layout = "rectangular",
layout.method = "equal_angle",
yscale = "none",
ladderize = TRUE,
right = FALSE,
Expand Down Expand Up @@ -265,6 +268,7 @@ fortify.codeml <- function(model, data,
##' @export
fortify.codeml_mlc <- function(model, data,
layout = "rectangular",
layout.method = "equal_angle",
yscale = "none",
ladderize = TRUE,
right = FALSE,
Expand Down Expand Up @@ -306,6 +310,7 @@ merge_phylo_anno.codeml_mlc <- function(df, dNdS, ndigits = NULL) {

fortify.codeml_mlc_ <- function(model, data,
layout = "rectangular",
layout.method = "equal_angle",
ladderize = TRUE,
right = FALSE,
branch.length = "branch.length",
Expand All @@ -317,8 +322,12 @@ fortify.codeml_mlc_ <- function(model, data,

##' @method fortify paml_rst
##' @export
fortify.paml_rst <- function(model, data, layout = "rectangular", yscale="none",
ladderize=TRUE, right=FALSE, mrsd=NULL, ...) {
fortify.paml_rst <- function(model, data,
layout = "rectangular",
yscale="none",
ladderize=TRUE,
right=FALSE,
mrsd=NULL, ...) {
df <- fortify.phylo(model@phylo, data, layout, ladderize, right, mrsd=mrsd, ...)
df <- merge_phylo_anno.paml_rst(df, model)
df <- scaleY(model@phylo, df, yscale, layout, ...)
Expand Down Expand Up @@ -353,8 +362,11 @@ fortify.hyphy <- fortify.paml_rst
##' @importFrom treeio get.placements
##' @export
fortify.jplace <- function(model, data,
layout="rectangular", yscale="none",
ladderize=TRUE, right=FALSE, mrsd=NULL, ...) {
layout="rectangular",
yscale="none",
ladderize=TRUE,
right=FALSE,
mrsd=NULL, ...) {
df <- extract.treeinfo.jplace(model, layout, ladderize, right, mrsd=mrsd, ...)
place <- get.placements(model, by="best")

Expand Down Expand Up @@ -403,8 +415,13 @@ fortify.phylo4 <- function(model, data, layout="rectangular", yscale="none",

##' @method fortify phylo4d
##' @export
fortify.phylo4d <- function(model, data, layout="rectangular", yscale="none",
ladderize=TRUE, right=FALSE, branch.length="branch.length",
fortify.phylo4d <- function(model, data,
layout="rectangular",
layout.method = "equal_angle",
yscale="none",
ladderize=TRUE,
right=FALSE,
branch.length="branch.length",
mrsd=NULL, ...) {
## model <- set_branch_length(model, branch.length)
## phylo <- as.phylo.phylo4(model)
Expand All @@ -413,7 +430,7 @@ fortify.phylo4d <- function(model, data, layout="rectangular", yscale="none",
## tdata <- model@data[match(res$node, rownames(model@data)), , drop=FALSE]
## df <- cbind(res, tdata)
## scaleY(as.phylo.phylo4(model), df, yscale, layout, ...)
fortify(as.treedata(model), data, layout, yscale, ladderize, right, branch.length, mrsd, ...)
fortify(as.treedata(model), data, layout, layout.method, yscale, ladderize, right, branch.length, mrsd, ...)
}


Expand All @@ -438,8 +455,12 @@ fortify.phylo4d <- function(model, data, layout="rectangular", yscale="none",
##' @method fortify phylo
##' @export
##' @author Yu Guangchuang
fortify.phylo <- function(model, data, layout="rectangular",
ladderize=TRUE, right=FALSE, mrsd=NULL, as.Date=FALSE, ...) {
fortify.phylo <- function(model, data,
layout="rectangular",
ladderize=TRUE,
right=FALSE,
mrsd=NULL,
as.Date=FALSE, ...) {
tree <- reorder.phylo(model, 'postorder')

if (ladderize == TRUE) {
Expand Down Expand Up @@ -605,18 +626,26 @@ fortify.multiPhylo <- function(model, data, layout="rectangular",

##' @method fortify phylip
##' @export
fortify.phylip <- function(model, data, layout="rectangular",
ladderize=TRUE, right=FALSE,
branch.length = "TREE", mrsd=NULL, ...) {
fortify.phylip <- function(model, data,
layout="rectangular",
layout.method = "equal_angle",
ladderize=TRUE,
right=FALSE,
branch.length = "TREE",
mrsd=NULL, ...) {
trees <- get.tree(model)
fortify(trees, layout=layout, ladderize = ladderize, right=right, mrsd=mrsd, ...)
}

##' @method fortify r8s
##' @export
fortify.r8s <- function(model, data, layout="rectangular",
ladderize=TRUE, right=FALSE,
branch.length = "TREE", mrsd=NULL, ...) {
fortify.r8s <- function(model, data,
layout="rectangular",
layout.method = "equal_angle",
ladderize=TRUE,
right=FALSE,
branch.length = "TREE",
mrsd=NULL, ...) {
trees <- get.tree(model)
branch.length %<>% match.arg(names(trees))
phylo <- trees[[branch.length]]
Expand All @@ -625,8 +654,11 @@ fortify.r8s <- function(model, data, layout="rectangular",

##' @method fortify obkData
##' @export
fortify.obkData <- function(model, data, layout="rectangular",
ladderize=TRUE, right=FALSE, mrsd = NULL, ...) {
fortify.obkData <- function(model, data,
layout="rectangular",
ladderize=TRUE,
right=FALSE,
mrsd = NULL, ...) {

df <- fortify(model@trees[[1]], layout=layout, ladderize=ladderize, right=right, mrsd=mrsd, ...)

Expand All @@ -644,8 +676,11 @@ fortify.obkData <- function(model, data, layout="rectangular",

##' @method fortify phyloseq
##' @export
fortify.phyloseq <- function(model, data, layout="rectangular",
ladderize=TRUE, right=FALSE, mrsd=NULL, ...) {
fortify.phyloseq <- function(model, data,
layout="rectangular",
ladderize=TRUE,
right=FALSE,
mrsd=NULL, ...) {

df <- fortify(model@phy_tree, layout=layout, ladderize=ladderize, right=right, mrsd=mrsd, ...)
phyloseq <- "phyloseq"
Expand Down
Loading