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Merged
merged 5 commits into from
Jul 11, 2025
Merged

consistency with upcoming ggplot2 version #657

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2b366a1
consistency with upcoming ggplot2 version
xiangpin Jun 20, 2025
1adac1d
consistency with upcoming ggplot2 version
xiangpin Jun 20, 2025
88dc31b
Merge branch 'master' of https://github.com/xiangpin/ggtree
xiangpin Jun 20, 2025
aca415c
avoid the error that could not find function is.waive
xiangpin Jun 26, 2025
1193ff8
using is_waiver codes avoid error when using old ggplot2 version
xiangpin Jul 11, 2025
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11 changes: 10 additions & 1 deletion R/geom_hilight.R
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Original file line number Diff line number Diff line change
Expand Up @@ -306,7 +306,16 @@ geom_hilight_encircle2 <- function(data=NULL,
)
}

check_linewidth <- getFromNamespace('check_linewidth', 'ggplot2')
check_linewidth <- function(data, name) {
if (is.null(data$linewidth) && !is.null(data$size)) {
warning(paste0(
"Using the `size` aesthetic with ", name, " was deprecated in ggplot2 3.4.0.\n",
"Please use the `linewidth` aesthetic instead."
))
data$linewidth <- data$size
}
data
}
snake_class <- getFromNamespace('snake_class', 'ggplot2')
snakeize <- getFromNamespace('snakeize', 'ggplot2')

Expand Down
15 changes: 13 additions & 2 deletions R/geom_segment.R
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Original file line number Diff line number Diff line change
Expand Up @@ -136,5 +136,16 @@ GeomSegmentGGtree <- ggproto("GeomSegmentGGtree", GeomSegment,
)


empty <- getFromNamespace("empty", "ggplot2")
`%||%` <- getFromNamespace("%||%", "ggplot2")
is_waiver <- function(x){
inherits(x, "waiver")
}

empty <- function(df){
is.null(df) || nrow(df) == 0 || ncol(df) == 0 || is_waiver(df)
}

`%||%` <- function (a, b){
if (!is.null(a))
a
else b
}
64 changes: 32 additions & 32 deletions R/method-ggplot-add.R
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
##' @importFrom ggplot2 ggplot_add
##' @method ggplot_add facet_xlim
##' @export
ggplot_add.facet_xlim <- function(object, plot, object_name) {
ggplot_add.facet_xlim <- function(object, plot, object_name, ...) {
var <- panel_col_var(plot)
free_x <- plot$facet$params$free$x
if (!is.null(free_x)) {
Expand All @@ -17,12 +17,12 @@ ggplot_add.facet_xlim <- function(object, plot, object_name) {
}

obj <- geom_blank(aes_(x = ~x), dummy, inherit.aes = FALSE)
ggplot_add(obj, plot, object_name)
ggplot_add(obj, plot, object_name, ...)
}

##' @method ggplot_add zoom_clade
##' @export
ggplot_add.zoom_clade <- function(object, plot, object_name) {
ggplot_add.zoom_clade <- function(object, plot, object_name, ...) {
zoomClade(plot, object$node, xexpand=object$xexpand)
}

Expand Down Expand Up @@ -83,17 +83,17 @@ ggplot_add.zoom_clade <- function(object, plot, object_name) {

##' @method ggplot_add geom_range
##' @export
ggplot_add.geom_range <- function(object, plot, object_name) {
ggplot_add.geom_range <- function(object, plot, object_name, ...) {
obj <- do.call(geom_range_internal, object)
assign(x = "range_range", value = object$range, envir = plot$plot_env)
assign(x = "range_center", value = object$center, envir = plot$plot_env)
ggplot_add(obj, plot, object_name)
ggplot_add(obj, plot, object_name, ...)
}

##' @method ggplot_add layout_ggtree
##' @importFrom ggplot2 expansion
##' @export
ggplot_add.layout_ggtree <- function(object, plot, object_name) {
ggplot_add.layout_ggtree <- function(object, plot, object_name, ...) {
if(object$layout == 'fan') {
return(open_tree(plot, object$angle))
}
Expand All @@ -115,7 +115,7 @@ ggplot_add.layout_ggtree <- function(object, plot, object_name) {
} else { ## rectangular
obj <- coord_cartesian(clip = 'off')
}
plot <- ggplot_add(obj, plot, object_name)
plot <- ggplot_add(obj, plot, object_name, ...)
plot$plot_env <- build_new_plot_env(plot$plot_env)
assign("layout", object$layout, envir = plot$plot_env)
return(plot)
Expand All @@ -125,7 +125,7 @@ ggplot_add.layout_ggtree <- function(object, plot, object_name) {

##' @method ggplot_add range_xaxis
##' @export
ggplot_add.range_xaxis <- function(object, plot, object_name) {
ggplot_add.range_xaxis <- function(object, plot, object_name, ...) {
d <- plot$data
center <- get("range_center", envir = plot$plot_env)
if (center == "auto") {
Expand All @@ -140,12 +140,12 @@ ggplot_add.range_xaxis <- function(object, plot, object_name) {

diff <- cc - d$x[i]
obj <- scale_x_continuous(sec.axis = ~. + diff)
ggplot_add(obj, plot, object_name)
ggplot_add(obj, plot, object_name, ...)
}

##' @method ggplot_add ggexpand
##' @export
ggplot_add.ggexpand <- function(object, plot, object_name) {
ggplot_add.ggexpand <- function(object, plot, object_name, ...) {
side <- object$side
obj <- NULL
if (side == 'h' || side == 'hv') {
Expand All @@ -157,7 +157,7 @@ ggplot_add.ggexpand <- function(object, plot, object_name) {
lim <- ggexpand_internal(plot, object$ratio, object$direction, 'y')
obj <- list(obj, ggplot2::expand_limits(y = lim))
}
ggplot_add(obj, plot, object_name)
ggplot_add(obj, plot, object_name, ...)
}

ggexpand_internal <- function(plot, ratio, direction, var) {
Expand All @@ -178,25 +178,25 @@ ggexpand_internal <- function(plot, ratio, direction, var) {

##' @method ggplot_add tree_inset
##' @export
ggplot_add.tree_inset <- function(object, plot, object_name) {
ggplot_add.tree_inset <- function(object, plot, object_name, ...) {
object$tree_view <- plot
do.call(inset, object)
}

##' @method ggplot_add facet_plot
##' @export
ggplot_add.facet_plot <- function(object, plot, object_name) {
ggplot_add.facet_plot <- function(object, plot, object_name, ...) {
plot <- add_panel(plot, object$panel)
df <- plot %+>% object$data
params <- c(list(data = df, mapping = object$mapping),
object$params)
obj <- do.call(object$geom, params)
ggplot_add(obj, plot, object_name)
ggplot_add(obj, plot, object_name, ...)
}

##' @method ggplot_add tiplab
##' @export
ggplot_add.tiplab <- function(object, plot, object_name) {
ggplot_add.tiplab <- function(object, plot, object_name, ...) {
layout <- get_layout(plot)
if (layout == 'dendrogram'){
if( object$hjust == 0 ){
Expand Down Expand Up @@ -227,7 +227,7 @@ ggplot_add.tiplab <- function(object, plot, object_name) {
#object$geom <- NULL
object$offset <- NULL
object$nodelab <- NULL
res <- ggplot_add.tiplab_ylab(object, plot, object_name)
res <- ggplot_add.tiplab_ylab(object, plot, object_name, ...)
return(res)
}

Expand All @@ -239,12 +239,12 @@ ggplot_add.tiplab <- function(object, plot, object_name) {
#object$nodelab <- NULL
ly <- do.call(geom_tiplab_rectangular, object)
}
ggplot_add(ly, plot, object_name)
ggplot_add(ly, plot, object_name, ...)
}

##' @method ggplot_add tiplab_ylab
##' @export
ggplot_add.tiplab_ylab <- function(object, plot, object_name) {
ggplot_add.tiplab_ylab <- function(object, plot, object_name, ...) {
layout <- get_layout(plot)
if (is.null(object$position)) {
if (layout == "rectangular") {
Expand Down Expand Up @@ -295,20 +295,20 @@ ggplot_add.tiplab_ylab <- function(object, plot, object_name) {

##' @method ggplot_add cladelabel
##' @export
ggplot_add.cladelabel <- function(object, plot, object_name) {
ggplot_add.cladelabel <- function(object, plot, object_name, ...) {
#layout <- get("layout", envir = plot$plot_env)
layout <- get_layout(plot)
if (layout == "unrooted" || layout == "daylight") {
ly <- do.call(geom_cladelabel2, object)
} else {
ly <- do.call(geom_cladelabel_rectangular, object)
}
ggplot_add(ly, plot, object_name)
ggplot_add(ly, plot, object_name, ...)
}

##' @method ggplot_add cladelab
##' @export
ggplot_add.cladelab <- function(object, plot, object_name){
ggplot_add.cladelab <- function(object, plot, object_name, ...){
#layout <- get("layout", envir=plot$plot_env)
layout <- get_layout(plot)
if (is.null(object$mapping) && (is.null(object$node) || is.null(object$label))){
Expand Down Expand Up @@ -433,7 +433,7 @@ ggplot_add.cladelab <- function(object, plot, object_name){
bar_obj <- do.call("geom_segment", bar_obj)
}
obj <- list(annot_obj, bar_obj)
ggplot_add(obj, plot, object_name)
ggplot_add(obj, plot, object_name, ...)
}

## ##' @method ggplot_add hilight
Expand Down Expand Up @@ -461,7 +461,7 @@ ggplot_add.cladelab <- function(object, plot, object_name){
##' @method ggplot_add hilight
##' @importFrom rlang quo_name
##' @export
ggplot_add.hilight <- function(object, plot, object_name){
ggplot_add.hilight <- function(object, plot, object_name, ...){
#layout <- get("layout", envir = plot$plot_env)
layout <- get_layout(plot)
if (!is.character(layout)) layout <- "rectangular"
Expand Down Expand Up @@ -572,7 +572,7 @@ ggplot_add.hilight <- function(object, plot, object_name){
roundrect = choose_hilight_layer(object = object, type = "roundrect")
)
}
plot <- ggplot_add(ly, plot, object_name)
plot <- ggplot_add(ly, plot, object_name, ...)
if (object$to.bottom){
idx <- length(plot$layers)
plot$layers <- c(plot$layers[idx], plot$layers[-idx])
Expand All @@ -583,7 +583,7 @@ ggplot_add.hilight <- function(object, plot, object_name){

##' @method ggplot_add striplabel
##' @export
ggplot_add.striplabel <- function(object, plot, object_name) {
ggplot_add.striplabel <- function(object, plot, object_name, ...) {
d <- plot$data
strip_df <- get_striplabel_position(d, object$taxa1, object$taxa2,
object$offset, object$align,
Expand Down Expand Up @@ -620,12 +620,12 @@ ggplot_add.striplabel <- function(object, plot, object_name) {
)
}

ggplot_add(list(ly_bar, ly_text), plot, object_name)
ggplot_add(list(ly_bar, ly_text), plot, object_name, ...)
}

##' @method ggplot_add striplab
##' @export
ggplot_add.striplab <- function(object, plot, object_name){
ggplot_add.striplab <- function(object, plot, object_name, ...){
layout <- get_layout(plot)
if (is.null(object$data) && is.null(object$taxa1) && is.null(object$taxa2) && is.null(object$label)){
abort("data and taxa1, taxa2, label can't be NULL simultaneously!")
Expand Down Expand Up @@ -739,14 +739,14 @@ ggplot_add.striplab <- function(object, plot, object_name){
bar_obj <- do.call("geom_segment", bar_obj)
#}
obj <- list(annot_obj, bar_obj)
ggplot_add(obj, plot, object_name)
ggplot_add(obj, plot, object_name, ...)
}

##' @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) {
ggplot_add.scale_ggtree <- function(object, plot, object_name, ...) {
mrsd <- get("mrsd", envir = plot$plot_env)
if (!is.null(mrsd) && inherits(plot$data$x, "Date")) {
x <- Date2decimal(plot$data$x)
Expand Down Expand Up @@ -789,13 +789,13 @@ ggplot_add.scale_ggtree <- function(object, plot, object_name) {
} else {
obj <- scale_x_continuous(breaks=breaks, labels=labels)
}
ggplot_add(obj, plot, object_name)
ggplot_add(obj, plot, object_name, ...)
}

##' @importFrom ggplot2 aes_
##' @importFrom rlang abort as_name
##' @export
ggplot_add.taxalink <- function(object, plot, object_name){
ggplot_add.taxalink <- function(object, plot, object_name, ...){
#layout <- get("layout", envir = plot$plot_env)
layout <- get_layout(plot)
if (object$outward=="auto"){
Expand Down Expand Up @@ -848,5 +848,5 @@ ggplot_add.taxalink <- function(object, plot, object_name){
}
params <- c(list(data=object$data, mapping=object$mapping, outward=object$outward), object$params)
obj <- do.call("geom_curvelink", params)
ggplot_add(obj, plot, object_name)
ggplot_add(obj, plot, object_name, ...)
}