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

 Package: ggtree

 Type: Package

 Title: an R package for visualization of tree and annotation data

-Version: 3.6.1

+Version: 3.6.2

 Authors@R: c(

        person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), 

             comment = c(ORCID = "0000-0002-6485-8781")),

@@ -38,7 +38,8 @@ Imports:

     treeio (>= 1.8.0),

     utils,

     scales,

-    stats

+    stats,

+    cli

 Suggests:

     emojifont,

     ggimage,

@@ -168,6 +168,7 @@ importFrom(ape,reorder.phylo)

 importFrom(ape,rtree)

 importFrom(aplot,plot_list)

 importFrom(aplot,xrange)

+importFrom(cli,cli_alert_warning)

 importFrom(dplyr,collapse)

 importFrom(dplyr,filter)

 importFrom(dplyr,full_join)

@@ -123,6 +123,7 @@ geom_hilight_rect2 <- function(data=NULL,

 #' @importFrom ggplot2 draw_key_polygon Geom ggproto aes GeomPolygon

 #' @importFrom grid rectGrob gpar grobTree

+#' @importFrom cli cli_alert_warning

 GeomHilightRect <- ggproto("GeomHilightRect", Geom,

                            default_aes = aes(colour = NA, fill = "steelblue", 

                                              linewidth = 0.5, linetype = 1, alpha = 0.5,

@@ -146,18 +147,16 @@ GeomHilightRect <- ggproto("GeomHilightRect", Geom,

                                    flag2 <- data$extendto < data$xmax

                                    flag <- equals(flag1, flag2)

                                    if (all(flag1) && any(flag)){

-                                       warning_wrap("extendto ", 

-                                                    paste0(data$extendto[flag], collapse="; "), 

-                                                    ifelse(length(data$extendto[flag])>1, " are", " is"), 

-                                                    " too small for node: ", paste0(data$clade_root_node[flag], collapse="; "),

-                                                    ", keep the original xmax value(s): ", paste0(data$xmax[flag], collapse="; "), ".")

+                                       cli_alert_warning(c("{.code extendto} ", paste0(data$extendto[flag], collapse="; "), 

+                                                    ifelse(length(data$extendto[flag])>1, " are", " is")," too small for node: ", 

+                                                    paste0(data$clade_root_node[flag], collapse="; "),", keep the original xmax value(s): ", 

+                                                    paste0(data$xmax[flag], collapse="; "), "."), wrap = TRUE)

                                        data$xmax[!flag] <- data$extendto[!flag]

                                    }else if(!all(flag1) && any(flag)){

-                                       warning_wrap("extendto ", 

-                                                    paste0(data$extendto[flag], collapse="; "), 

-                                                    ifelse(length(data$extendto[flag])>1, " are", " is"),

-                                                    " too big for node: ", paste0(data$clade_root_node[flag], collapse="; "),

-                                                    ", keep the original xmax value(s): ", paste0(data$xmax[flag], collapse="; "), ".")

+                                       cli_alert_warning(c("{.code extendto} ", paste0(data$extendto[flag], collapse="; "), 

+                                                    ifelse(length(data$extendto[flag])>1, " are", " is"), " too big for node: ", 

+                                                    paste0(data$clade_root_node[flag], collapse="; "), ", keep the original xmax value(s): ", 

+                                                    paste0(data$xmax[flag], collapse="; "), "."), wrap = TRUE)

                                        data$xmax[!flag] <- data$extendto[!flag]

                                    }else{

                                        data$xmax <- data$extendto 

@@ -166,10 +165,12 @@ GeomHilightRect <- ggproto("GeomHilightRect", Geom,

                                data <- build_align_data(data=data, align=align) 

                                if (!coord$is_linear()) {

                                    if (gradient){

-                                       warning_wrap("The gradient color hight light layer only presents in rectangular, ellipse, roundrect layouts")

+                                       cli_alert_warning("The gradient color hight light layer only presents in 

+                                                         rectangular, ellipse, roundrect layouts.", wrap = TRUE)

                                    }

                                    if (roundrect){

-                                       warning_wrap("The round rectangular hight light layer only presents in rectangular, ellipse, roundrect layouts")

+                                       cli_alert_warning("The round rectangular hight light layer only presents in 

+                                                         rectangular, ellipse, roundrect layouts.", wrap =TRUE)

                                    }

                                    aesthetics <- setdiff(colnames(data), #"x.start", "y.start", "x.stop", "y.stop"), 

                                                          c("xmin", "xmax", "ymin", "ymax", "clade_root_node"))

@@ -212,7 +213,7 @@ GeomHilightRect <- ggproto("GeomHilightRect", Geom,

                                    hilightGrob <- ifelse(roundrect, grid::roundrectGrob, grid::rectGrob)

                                    if (gradient){

                                        if (roundrect){

-                                           warning_wrap("The round rectangular and gradient are not applied simultaneously")

+                                           cli_alert_warning("The round rectangular and gradient are not applied simultaneously")

                                        }

                                        gradient.direction <- match.arg(gradient.direction, c("rt", "tr"))

                                        rects <- lapply(split(coords, seq_len(nrow(coords))), function(row){

@@ -304,6 +305,10 @@ geom_hilight_encircle2 <- function(data=NULL,

           )

 }

+check_linewidth <- getFromNamespace('check_linewidth', 'ggplot2')

+snake_class <- getFromNamespace('snake_class', 'ggplot2')

+snakeize <- getFromNamespace('snakeize', 'ggplot2')

+

 GeomHilightEncircle <- ggproto("GeomHilightEncircle", Geom,

                                 required_aes = c("x", "y", "clade_root_node"),

                                 default_aes = aes(colour="black", fill="steelblue", alpha = 0.5,

@@ -311,7 +316,8 @@ GeomHilightEncircle <- ggproto("GeomHilightEncircle", Geom,

                                                   s_shape=0.5, s_open=FALSE),

                                 draw_key = draw_key_polygon,

                                 rename_size = TRUE,

-                                draw_panel = function(data, panel_scales, coord){

+                                draw_panel = function(self, data, panel_scales, coord){

+                                    data <- check_linewidth(data, snake_class(self))

                                     globs <- lapply(split(data, data$clade_root_node), function(i)

                                                    get_glob_encircle(i, panel_scales, coord))

                                     ggname("geom_hilight_encircle2", do.call("grobTree", globs))

@@ -477,14 +483,7 @@ build_align_data <- function(data, align){

 #' @importFrom utils getFromNamespace

-#warning_wrap <- getFromNamespace("warning_wrap", "ggplot2")

-warning_wrap <- function(...){

-    x = paste0(...)

-    x = paste(strwrap(x), collapse = "\n")

-    warning(x, call. = FALSE)

-}

 rect_to_poly <- getFromNamespace("rect_to_poly", "ggplot2")

-#new_data_frame <- getFromNamespace("new_data_frame", "ggplot2")

 ## ##' layer of hilight clade with rectangle

 ## ##'

@@ -139,7 +139,7 @@ get_glob_encircle <- function(data, panel_scales, coord){

     data.frame(x,y,first_row[!names(first_row) %in% c("x","y")])

   }

-  coords <- coords[ch,]

+  coords <- coords[ch,,drop=FALSE]

   ## FIXME: using grid:: a lot. importFrom instead?

   ## convert from lengths to physical units, for computing *directions*

@@ -195,7 +195,8 @@ get_glob_encircle <- function(data, panel_scales, coord){

   ## browser()

   gp <- grid::get.gpar()

-  pars1 <- c("colour","linetype","alpha","fill","size")

+  # the 'size' of line in ggplot2 3.4.0 have been replaced with 'linewidth'

+  pars1 <- c("colour","linetype","alpha","fill","linewidth")

   pars2 <- c("col","lty","alpha","fill","lwd")

   gp[pars2] <- first_row[pars1]

   grid::xsplineGrob(

@@ -133,10 +133,11 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE,

     params <- list(...)

     if ("nudge_x" %in% names(params)){

         if (offset != 0){

-            warning_wrap("Both nudge_x and offset arguments are provided.

+            cli_alert_warning("Both {.code nudge_x} and {.code offset} arguments are provided.

                          Because they all adjust the horizontal offset of labels,

-                         and the 'nudge_x' is consistent with 'ggplot2'. The

-                         'offset' will be deprecated here and only the 'nudge_x' will be used.")

+                         and the {.code nudge_x} is consistent with {.code ggplot2}. The

+                         {.code offset} will be deprecated here and only the {.code nudge_x} will be used.", 

+                         wrap = TRUE)

         }

         offset <- params$nudge_x

         params$nudge_x <- NULL

@@ -39,14 +39,10 @@

 ##' <http://yulab-smu.top/treedata-book/index.html> by Guangchuang Yu.

 geom_tree <- function(mapping=NULL, data=NULL, layout="rectangular", multiPhylo=FALSE, continuous="none", position="identity", ...) {

     if (is.logical(continuous)){

-        warning_wrap('The type of "continuous" argument was changed (v>=2.5.2). Now, 

-                     it should be one of "color" (or "colour"), "size", "all", and "none".')

-        ifelse(continuous,

-               warning_wrap('It was set to TRUE, it should be replaced with "color" (or "colour"), 

-                            this meaning the aesthethic of "color" (or "colour") is continuous.'),

-               warning_wrap('It was set to FALSE, it should be replaced with "none", 

-                            this meaning the aesthethic of "color" (or "colour") or "size" will not be continuous.')

-        )

+        cli::cli_warn(c("The type of {.code continuous} argument was changed (v>=2.5.2). Now,", 

+                        "i" = "Consider using {.code continuous = \"color\"}, {.code continuous = \"colour\"}, ", 

+                        "{.code continuous = \"size\"}, {.code continuous = \"all\"} or",

+                        " {.code continuous = \"none\"} instead."))

         continuous <- ifelse(continuous, "color", "none")

     }

     continuous <- match.arg(continuous, c("color", "colour", "size", "none", "all"))

@@ -100,7 +100,7 @@ nodebar <- function(data, cols, color, alpha=1, position="stack") {

                                      theme_inset()

                    )

-    if (missingArg(color) || is.null(color) || is.na(color)) {

+    if (missingArg(color) || is.null(color) || any(is.na(color))) {

         ## do nothing

     } else {

         bars <- lapply(bars, function(p) p+scale_fill_manual(values=color))

@@ -345,8 +345,9 @@ ggplot_add.cladelab <- function(object, plot, object_name){

                 samevars <- Reduce(intersect,list(extract_all_aes_var(object$mapping), colnames(plot$data), colnames(object$data)))

                 object$data <- merge(object$data, plot$data, by.x=quo_name(object$mapping$node), by.y="node", all.x=TRUE)

                 if (length(samevars) > 0){

-                    warning_wrap('The "', paste(samevars, collapse=", ") ,'" has(have) been found in tree data. You might need to 

-                                 rename the variable(s) in the data of "geom_cladelab" to avoid this warning!')

+                    cli_alert_warning(text=c('The "', paste(samevars, collapse=", ") ,'" has(have) been found in tree data. You might need to 

+                                 rename the variable(s) in the data of "geom_cladelab" to avoid this warning!'),

+                                 wrap = TRUE)

                     object$mapping <- remapping(mapping=object$mapping, samevars=samevars)

                 }

             }

@@ -504,8 +505,10 @@ ggplot_add.hilight <- function(object, plot, object_name){

                      samevars <- Reduce(intersect,list(extract_all_aes_var(object$mapping), colnames(plot$data), colnames(object$data)))

                      object$data <- merge(object$data, plot$data, by.x=quo_name(object$mapping$node), by.y="node", all.x=TRUE)

                      if (length(samevars) > 0){

-                         warning_wrap('The "', paste(samevars, collapse=", ") ,'" has(have) been found in tree data. You might need to 

-                                      rename the variable(s) in the data of "geom_hilight" to avoid this warning!')

+                         cli_alert_warning(text=c('The "', paste(samevars, collapse=", ") ,'" has(have) been found in tree data. You might need to 

+                                      rename the variable(s) in the data of "geom_hilight" to avoid this warning!'),

+                                      wrap = TRUE

+                                     )

                          object$mapping <- remapping(mapping=object$mapping, samevars=samevars)

                      }

                  }

@@ -42,7 +42,9 @@ layoutEqualAngle <- function(model, branch.length = "branch.length"){

   if (! is.null(tree$edge.length)) {

       if (anyNA(tree$edge.length)) {

-          warning("'edge.length' contains NA values...\n## setting 'edge.length' to NULL automatically when plotting the tree...")

+          cli_alert_warning(c("{.code edge.length} contains NA values...",

+                          "## setting {.code edge.length} of the tree to NULL ",

+                          "automatically when plotting the tree..."), wrap = TRUE)

           tree$edge.length <- NULL

       }

   }

@@ -771,12 +773,10 @@ getXcoord2 <- function(x, root, parent, child, len, start=0, rev=FALSE) {

     ignore_negative_edge <- getOption("ignore.negative.edge", default=FALSE)

     if (any(len < 0) && !ignore_negative_edge) {

-        warning_wrap("The tree contained negative ", 

-                     ifelse(sum(len < 0)>1, "edge lengths", "edge length"),

-                     ". If you want to ignore the ", 

-                     ifelse(sum(len<0) > 1, "edges", "edge"),

-                     ", you can set 'options(ignore.negative.edge=TRUE)', then re-run ggtree."

-                     )

+        cli_alert_warning(c("The tree contained negative ", ifelse(sum(len < 0)>1, "edge lengths", "edge length"), 

+                        ". If you want to ignore the ", ifelse(sum(len<0) > 1, "edges", "edge"), ", you can 

+                        set {.code options(ignore.negative.edge=TRUE)}, then re-run ggtree."

+                     ), wrap = TRUE)

     }

     while(anyNA(x)) {

         idx <- which(parent %in% currentNode)