@@ -25,7 +25,7 @@ Imports:

     ape,

     aplot,

     dplyr,

-    ggplot2 (>= 3.0.0),

+    ggplot2 (> 3.3.6),

     grid,

     magrittr,

     methods,

@@ -38,7 +38,7 @@

 #'        \item \code{extend} extend xmax of the rectangle, defaults to 0.

 #'        \item \code{extendto} specify a value, meaning the rectangle extend to, defaults to NULL.

 #'        \item \code{linetype} the line type of margin, defaults to 1.

-#'        \item \code{size} the width of line of margin, defaults to 0.5.

+#'        \item \code{linewidth} the width of line of margin, defaults to 0.5.

 #'     }

 #' \code{geom_hilight()} understands the following aesthethics for encircle layer (required 

 #' aesthetics are in bold):

@@ -49,7 +49,7 @@

 #'        \item \code{alpha} the transparency of fill, defaults to 0.5.

 #'        \item \code{expand} expands the xspline clade region, defaults to 0.

 #'        \item \code{spread} control the size, when only one point.

-#'        \item \code{size} the width of line of margin, defaults to 0.5.

+#'        \item \code{linewidth} the width of line of margin, defaults to 0.5.

 #'        \item \code{linetype} the line type of margin, defaults to 1.

 #'        \item \code{s_shape} the shape of the spline relative to the control points, defaults to 0.5.

 #'        \item \code{s_open}  whether the spline is a line or a closed shape, defaults to FALSE.

@@ -125,10 +125,11 @@ geom_hilight_rect2 <- function(data=NULL,

 #' @importFrom grid rectGrob gpar grobTree

 GeomHilightRect <- ggproto("GeomHilightRect", Geom,

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

-                                             size = 0.5, linetype = 1, alpha = 0.5,

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

                                              extend=0, extendto=NULL),

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

                            draw_key = draw_key_polygon,

+                           rename_size = TRUE,

                            draw_panel = function(self, data, panel_params, coord, 

                                                  linejoin = "mitre", align="none", 

                                                  gradient = FALSE, 

@@ -195,7 +196,7 @@ GeomHilightRect <- ggproto("GeomHilightRect", Geom,

                                    #data <- data %>% dplyr::left_join(df, by="clade_root_node")

                                    polys <- lapply(split(data, seq_len(nrow(data))), function(row) {

                                                  poly <- rect_to_poly(row$xmin, row$xmax, row$ymin, row$ymax)

-                                                 aes <- new_data_frame(row[aesthetics])[rep(1,5), ]

+                                                 aes <- row[rep(1,5), aesthetics] 

                                                  #draw_panel_polar(data = cbind(poly, aes), 

                                                  #                 panel_params = panel_params, 

                                                  #                 coord = coord, 

@@ -203,7 +204,7 @@ GeomHilightRect <- ggproto("GeomHilightRect", Geom,

                                                  #                 gradient.direction = gradient.direction,

                                                  #                 gradient.length.out = gradient.length.out

                                                  #   )

-                                                 GeomPolygon$draw_panel(cbind(poly, aes), panel_params, coord)

+                                                 GeomPolygon$draw_panel(vctrs::vec_cbind(poly, aes), panel_params, coord)

                                                  })

                                    ggname("geom_hilight_rect2", do.call("grobTree", polys))

                                }else{

@@ -235,7 +236,7 @@ GeomHilightRect <- ggproto("GeomHilightRect", Geom,

                                                          just = c("left", "top"),

                                                          gp = gpar(col = row$colour,

                                                                    fill = fill,

-                                                                   lwd = row$size * ggplot2:::.pt,

+                                                                   lwd = row$linewidth * ggplot2:::.pt,

                                                                    lty = row$linetype,

                                                                    linejoin = linejoin,

                                                                    lineend = if (identical(linejoin, "round")) "round" else "square")

@@ -255,7 +256,7 @@ GeomHilightRect <- ggproto("GeomHilightRect", Geom,

                                                             gp = grid::gpar(

                                                               col = row$colour,

                                                               fill = alpha(row$fill, row$alpha),

-                                                              lwd = row$size * ggplot2::.pt,

+                                                              lwd = row$linewidth * ggplot2::.pt,

                                                               lty = row$linetype,

                                                               lineend = "butt"

                                                             )

@@ -271,7 +272,7 @@ GeomHilightRect <- ggproto("GeomHilightRect", Geom,

                                                   just = c("left", "top"),

                                                   gp = gpar(col = coords$colour,

                                                             fill = alpha(coords$fill, coords$alpha),

-                                                            lwd = coords$size * ggplot2:::.pt,

+                                                            lwd = coords$linewidth * ggplot2:::.pt,

                                                             lty = coords$linetype,

                                                             linejoin = linejoin,

                                                             lineend = if (identical(linejoin, "round")) "round" else "square")

@@ -306,9 +307,10 @@ geom_hilight_encircle2 <- function(data=NULL,

 GeomHilightEncircle <- ggproto("GeomHilightEncircle", Geom,

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

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

-                                                  expand=0, spread=0.1, linetype=1, size=0.5,

+                                                  expand=0, spread=0.1, linetype=1, linewidth = 0.5,

                                                   s_shape=0.5, s_open=FALSE),

                                 draw_key = draw_key_polygon,

+                                rename_size = TRUE,

                                 draw_panel = function(data, panel_scales, coord){

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

                                                    get_glob_encircle(i, panel_scales, coord))

@@ -477,9 +479,14 @@ build_align_data <- function(data, align){

 #' @importFrom utils getFromNamespace

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

+#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")

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

 ## ##' layer of hilight clade with rectangle

 ## ##'

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

 ##' @title geom_range

 ##' @param range range(interval) to be displayed, e.g. "height_0.95_HPD"

 ##' @param center center of the range, mean, median or auto (default, the center of the range)

-##' @param ... additional parameter, e.g. color, size, alpha

+##' @param ... additional parameter, e.g. color, linewidth, alpha

 ##' @return ggplot layer

 ##' @importFrom ggplot2 aes_string

 ##' @export

@@ -7,12 +7,12 @@

 ##' @title geom_aline

 ##' @param mapping aes mapping

 ##' @param linetype set line type of the line, defaults to "dotted"

-##' @param size set line size of the line, defaults to 1

+##' @param linewidth set width of the line, defaults to 1

 ##' @param ... additional parameter

 ##' @return aline layer

 ##' @export

 ##' @author Yu Guangchuang

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

+geom_aline <- function(mapping=NULL, linetype="dotted", linewidth = 1, ...) {

     x <- y <- isTip <- NULL

     dot_mapping <- aes(xend=x+diff(range(x))/200, x=max(x), yend=y, subset=isTip)

     if (!is.null(mapping)) {

@@ -21,7 +21,7 @@ geom_aline <- function(mapping=NULL, linetype="dotted", size=1, ...) {

     geom_segment2(dot_mapping,

                   linetype=linetype,

-                  size=size, stat = StatTreeData, ...)

+                  linewidth = linewidth, stat = StatTreeData, ...)

 }

@@ -98,7 +98,7 @@ GeomSegmentGGtree <- ggproto("GeomSegmentGGtree", GeomSegment,

                                  data$x <- data$x + nudge_x

                                  data <- ggplot2::remove_missing(data, na.rm = na.rm, c("x", "y", "xend",

-                                                        "yend", "linetype", "size", "shape"), name = "geom_segment")

+                                                        "yend", "linetype", "linewidth", "shape"), name = "geom_segment")

                                  if (empty(data))

                                      return(zeroGrob())

                                  if (!coord$is_linear()) {

@@ -123,7 +123,7 @@ GeomSegmentGGtree <- ggproto("GeomSegmentGGtree", GeomSegment,

                                  return(grid::segmentsGrob(data$x, data$y, data$xend, data$yend,

                                                            default.units = "native", gp = gpar(col = alpha(data$colour,

                                                            data$alpha), fill = alpha(arrow.fill, data$alpha),

-                                                           lwd = data$size * ggplot2::.pt, lty = data$linetype,

+                                                           lwd = data$linewidth * ggplot2::.pt, lty = data$linetype,

                                                            lineend = lineend, linejoin = linejoin), arrow = arrow)

                                        )

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

 #' link between taxa 

 #'

 #' `geom_taxalink` supports data.frame as input,

-#' the `colour`, `size`, `linetype` and `alpha` can be mapped. When the `data` was provided, 

+#' the `colour`, `linewidth`, `linetype` and `alpha` can be mapped. When the `data` was provided, 

 #' the `mapping` should be also provided, which `taxa1` and `taxa2` should be mapped created 

 #' by `aes`, `aes_` or `aes_string`. In addition, the `hratio`, control the height of curve line, 

 #' when tree layout is `cirular`, default is 1. `ncp`, the number of control points used to draw the 

@@ -25,7 +25,7 @@

 #'        \item \code{group} group category of link.

 #'        \item \code{colour} control the color of line, default is black.

 #'        \item \code{linetype} control the type of line, default is 1 (solid).

-#'        \item \code{size} control the width of line, default is 0.5.

+#'        \item \code{linewidth} control the width of line, default is 0.5.

 #'        \item \code{curvature} control the curvature of line, default is 0.5, 

 #'        it will be created automatically in polar coordinate .

 #'        \item \code{hratio} control the height of curve line, default is 1.

@@ -175,7 +175,8 @@ geom_curvelink <- function(data=NULL,

 #' @importFrom scales alpha

 GeomCurvelink <- ggproto("GeomCurvelink", GeomSegment,

   required_aes = c("x", "y", "xend", "yend"),

-  default_aes = aes(colour = "black", size = 0.5, linetype = 1, alpha = NA, curvature=0.5, hratio=1, ncp=1, curveangle=90, square=FALSE),

+  default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = NA, curvature=0.5, hratio=1, ncp=1, curveangle=90, square=FALSE),

+  rename_size = TRUE,

   draw_panel = function(data, panel_params, coord, shape=0.5, outward=TRUE,

                         arrow = NULL, arrow.fill=NULL, lineend = "butt", na.rm = FALSE) {

     if (!coord$is_linear()) {

@@ -218,7 +219,7 @@ GeomCurvelink <- ggproto("GeomCurvelink", GeomSegment,

                               square = trans$square[i], squareShape = 1, inflect = FALSE, open = TRUE,

                               gp = gpar(col = alpha(trans$colour[i], trans$alpha[i]),

                                         fill = alpha(arrow.fill[i], trans$alpha[i]),

-                                        lwd = trans$size[i] * ggplot2::.pt,

+                                        lwd = trans$linewidth[i] * ggplot2::.pt,

                                         lty = trans$linetype[i],

                                         lineend = lineend),

                               arrow = arrow,

@@ -17,7 +17,7 @@

 ##' to the left side of tip labels, defaults to "FALSE"

 ##' with a line connecting each tip and its corresponding label, defaults to "FALSE"

 ##' @param linetype set linetype of the line if align = TRUE, defaults to "dotted"

-##' @param linesize set line size of the line if align = TRUE, defaults to 0.5

+##' @param linesize set line width if align = TRUE, defaults to 0.5

 ##' @param geom one of 'text', 'label', 'shadowtext', 'image' and 'phylopic'

 ##' @param as_ylab display tip labels as y-axis label, 

 ##' only works for rectangular and dendrogram layouts, defaults to "FALSE"

@@ -207,7 +207,7 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE,

                                     "bg.colour", "bg.r"))

     list(

         if (show_segment){

-            lineparams <- list(mapping = segment_mapping, linetype=linetype, nudge_x = offset, size = linesize, stat = StatTreeData)

+            lineparams <- list(mapping = segment_mapping, linetype=linetype, nudge_x = offset, linewidth = linesize, stat = StatTreeData)

             lineparams <- extract_params(lineparams, params, c("data", "color", "colour", "alpha", "show.legend", "na.rm",

                                                                "inherit.aes", "arrow", "arrow.fill", "lineend")) 

             do.call("geom_segment2", lineparams)

@@ -74,7 +74,7 @@ aesthetics are in bold):

 \item \code{extend} extend xmax of the rectangle, defaults to 0.

 \item \code{extendto} specify a value, meaning the rectangle extend to, defaults to NULL.

 \item \code{linetype} the line type of margin, defaults to 1.

-\item \code{size} the width of line of margin, defaults to 0.5.

+\item \code{linewidth} the width of line of margin, defaults to 0.5.

 }

 \code{geom_hilight()} understands the following aesthethics for encircle layer (required

 aesthetics are in bold):

@@ -85,7 +85,7 @@ aesthetics are in bold):

 \item \code{alpha} the transparency of fill, defaults to 0.5.

 \item \code{expand} expands the xspline clade region, defaults to 0.

 \item \code{spread} control the size, when only one point.

-\item \code{size} the width of line of margin, defaults to 0.5.

+\item \code{linewidth} the width of line of margin, defaults to 0.5.

 \item \code{linetype} the line type of margin, defaults to 1.

 \item \code{s_shape} the shape of the spline relative to the control points, defaults to 0.5.

 \item \code{s_open}  whether the spline is a line or a closed shape, defaults to FALSE.

@@ -4,14 +4,14 @@

 \alias{geom_aline}

 \title{geom_aline}

 \usage{

-geom_aline(mapping = NULL, linetype = "dotted", size = 1, ...)

+geom_aline(mapping = NULL, linetype = "dotted", linewidth = 1, ...)

 }

 \arguments{

 \item{mapping}{aes mapping}

 \item{linetype}{set line type of the line, defaults to "dotted"}

-\item{size}{set line size of the line, defaults to 1}

+\item{linewidth}{set width of the line, defaults to 1}

 \item{...}{additional parameter}

 }

@@ -11,7 +11,7 @@ geom_range(range, center = "auto", ...)

 \item{center}{center of the range, mean, median or auto (default, the center of the range)}

-\item{...}{additional parameter, e.g. color, size, alpha}

+\item{...}{additional parameter, e.g. color, linewidth, alpha}

 }

 \value{

 ggplot layer

@@ -36,7 +36,7 @@ a list object.

 }

 \description{

 \code{geom_taxalink} supports data.frame as input,

-the \code{colour}, \code{size}, \code{linetype} and \code{alpha} can be mapped. When the \code{data} was provided,

+the \code{colour}, \code{linewidth}, \code{linetype} and \code{alpha} can be mapped. When the \code{data} was provided,

 the \code{mapping} should be also provided, which \code{taxa1} and \code{taxa2} should be mapped created

 by \code{aes}, \code{aes_} or \code{aes_string}. In addition, the \code{hratio}, control the height of curve line,

 when tree layout is \code{cirular}, default is 1. \code{ncp}, the number of control points used to draw the

@@ -52,7 +52,7 @@ a column of data.

 \item \code{group} group category of link.

 \item \code{colour} control the color of line, default is black.

 \item \code{linetype} control the type of line, default is 1 (solid).

-\item \code{size} control the width of line, default is 0.5.

+\item \code{linewidth} control the width of line, default is 0.5.

 \item \code{curvature} control the curvature of line, default is 0.5,

 it will be created automatically in polar coordinate .

 \item \code{hratio} control the height of curve line, default is 1.

@@ -27,7 +27,7 @@ with a line connecting each tip and its corresponding label, defaults to "FALSE"

 \item{linetype}{set linetype of the line if align = TRUE, defaults to "dotted"}

-\item{linesize}{set line size of the line if align = TRUE, defaults to 0.5}

+\item{linesize}{set line width if align = TRUE, defaults to 0.5}

 \item{geom}{one of 'text', 'label', 'shadowtext', 'image' and 'phylopic'}