Browse code

rename size aesthetic according to ggplot2 (3.4.0)

xiangpin authored on 07/07/2022 12:57:13
Showing11 changed files

... ...
@@ -25,7 +25,7 @@ Imports:
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     ape,
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     aplot,
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     dplyr,
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-    ggplot2 (>= 3.0.0),
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+    ggplot2 (> 3.3.6),
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     grid,
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     magrittr,
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     methods,
... ...
@@ -38,7 +38,7 @@
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 #'        \item \code{extend} extend xmax of the rectangle, defaults to 0.
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 #'        \item \code{extendto} specify a value, meaning the rectangle extend to, defaults to NULL.
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 #'        \item \code{linetype} the line type of margin, defaults to 1.
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-#'        \item \code{size} the width of line of margin, defaults to 0.5.
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+#'        \item \code{linewidth} the width of line of margin, defaults to 0.5.
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 #'     }
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 #' \code{geom_hilight()} understands the following aesthethics for encircle layer (required 
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 #' aesthetics are in bold):
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@@ -49,7 +49,7 @@
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 #'        \item \code{alpha} the transparency of fill, defaults to 0.5.
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 #'        \item \code{expand} expands the xspline clade region, defaults to 0.
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 #'        \item \code{spread} control the size, when only one point.
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-#'        \item \code{size} the width of line of margin, defaults to 0.5.
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+#'        \item \code{linewidth} the width of line of margin, defaults to 0.5.
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 #'        \item \code{linetype} the line type of margin, defaults to 1.
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 #'        \item \code{s_shape} the shape of the spline relative to the control points, defaults to 0.5.
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 #'        \item \code{s_open}  whether the spline is a line or a closed shape, defaults to FALSE.
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@@ -125,10 +125,11 @@ geom_hilight_rect2 <- function(data=NULL,
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 #' @importFrom grid rectGrob gpar grobTree
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 GeomHilightRect <- ggproto("GeomHilightRect", Geom,
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                            default_aes = aes(colour = NA, fill = "steelblue", 
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-                                             size = 0.5, linetype = 1, alpha = 0.5,
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+                                             linewidth = 0.5, linetype = 1, alpha = 0.5,
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                                              extend=0, extendto=NULL),
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                            required_aes = c("xmin", "xmax", "ymin", "ymax", "clade_root_node"),
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                            draw_key = draw_key_polygon,
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+                           rename_size = TRUE,
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                            draw_panel = function(self, data, panel_params, coord, 
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                                                  linejoin = "mitre", align="none", 
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                                                  gradient = FALSE, 
... ...
@@ -195,7 +196,7 @@ GeomHilightRect <- ggproto("GeomHilightRect", Geom,
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                                    #data <- data %>% dplyr::left_join(df, by="clade_root_node")
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                                    polys <- lapply(split(data, seq_len(nrow(data))), function(row) {
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                                                  poly <- rect_to_poly(row$xmin, row$xmax, row$ymin, row$ymax)
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-                                                 aes <- new_data_frame(row[aesthetics])[rep(1,5), ]
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+                                                 aes <- row[rep(1,5), aesthetics] 
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                                                  #draw_panel_polar(data = cbind(poly, aes), 
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                                                  #                 panel_params = panel_params, 
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                                                  #                 coord = coord, 
... ...
@@ -203,7 +204,7 @@ GeomHilightRect <- ggproto("GeomHilightRect", Geom,
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                                                  #                 gradient.direction = gradient.direction,
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                                                  #                 gradient.length.out = gradient.length.out
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                                                  #   )
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-                                                 GeomPolygon$draw_panel(cbind(poly, aes), panel_params, coord)
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+                                                 GeomPolygon$draw_panel(vctrs::vec_cbind(poly, aes), panel_params, coord)
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                                                  })
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                                    ggname("geom_hilight_rect2", do.call("grobTree", polys))
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                                }else{
... ...
@@ -235,7 +236,7 @@ GeomHilightRect <- ggproto("GeomHilightRect", Geom,
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                                                          just = c("left", "top"),
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                                                          gp = gpar(col = row$colour,
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                                                                    fill = fill,
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-                                                                   lwd = row$size * ggplot2:::.pt,
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+                                                                   lwd = row$linewidth * ggplot2:::.pt,
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                                                                    lty = row$linetype,
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                                                                    linejoin = linejoin,
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                                                                    lineend = if (identical(linejoin, "round")) "round" else "square")
... ...
@@ -255,7 +256,7 @@ GeomHilightRect <- ggproto("GeomHilightRect", Geom,
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                                                             gp = grid::gpar(
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                                                               col = row$colour,
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                                                               fill = alpha(row$fill, row$alpha),
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-                                                              lwd = row$size * ggplot2::.pt,
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+                                                              lwd = row$linewidth * ggplot2::.pt,
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                                                               lty = row$linetype,
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                                                               lineend = "butt"
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                                                             )
... ...
@@ -271,7 +272,7 @@ GeomHilightRect <- ggproto("GeomHilightRect", Geom,
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                                                   just = c("left", "top"),
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                                                   gp = gpar(col = coords$colour,
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                                                             fill = alpha(coords$fill, coords$alpha),
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-                                                            lwd = coords$size * ggplot2:::.pt,
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+                                                            lwd = coords$linewidth * ggplot2:::.pt,
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                                                             lty = coords$linetype,
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                                                             linejoin = linejoin,
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                                                             lineend = if (identical(linejoin, "round")) "round" else "square")
... ...
@@ -306,9 +307,10 @@ geom_hilight_encircle2 <- function(data=NULL,
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 GeomHilightEncircle <- ggproto("GeomHilightEncircle", Geom,
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                                 required_aes = c("x", "y", "clade_root_node"),
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                                 default_aes = aes(colour="black", fill="steelblue", alpha = 0.5,
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-                                                  expand=0, spread=0.1, linetype=1, size=0.5,
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+                                                  expand=0, spread=0.1, linetype=1, linewidth = 0.5,
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                                                   s_shape=0.5, s_open=FALSE),
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                                 draw_key = draw_key_polygon,
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+                                rename_size = TRUE,
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                                 draw_panel = function(data, panel_scales, coord){
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                                     globs <- lapply(split(data, data$clade_root_node), function(i)
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                                                    get_glob_encircle(i, panel_scales, coord))
... ...
@@ -475,9 +477,14 @@ build_align_data <- function(data, align){
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 #' @importFrom utils getFromNamespace
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-warning_wrap <- getFromNamespace("warning_wrap", "ggplot2")
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+#warning_wrap <- getFromNamespace("warning_wrap", "ggplot2")
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+warning_wrap <- function(...){
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+    x = paste0(...)
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+    x = paste(strwrap(x), collapse = "\n")
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+    warning(x, call. = FALSE)
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+}
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 rect_to_poly <- getFromNamespace("rect_to_poly", "ggplot2")
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-new_data_frame <- getFromNamespace("new_data_frame", "ggplot2")
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+#new_data_frame <- getFromNamespace("new_data_frame", "ggplot2")
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 ## ##' layer of hilight clade with rectangle
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 ## ##'
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@@ -4,7 +4,7 @@
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 ##' @title geom_range
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 ##' @param range range(interval) to be displayed, e.g. "height_0.95_HPD"
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 ##' @param center center of the range, mean, median or auto (default, the center of the range)
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-##' @param ... additional parameter, e.g. color, size, alpha
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+##' @param ... additional parameter, e.g. color, linewidth, alpha
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 ##' @return ggplot layer
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 ##' @importFrom ggplot2 aes_string
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 ##' @export
... ...
@@ -7,12 +7,12 @@
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 ##' @title geom_aline
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 ##' @param mapping aes mapping
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 ##' @param linetype set line type of the line, defaults to "dotted"
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-##' @param size set line size of the line, defaults to 1
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+##' @param linewidth set width of the line, defaults to 1
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 ##' @param ... additional parameter
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 ##' @return aline layer
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 ##' @export
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 ##' @author Yu Guangchuang
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-geom_aline <- function(mapping=NULL, linetype="dotted", size=1, ...) {
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+geom_aline <- function(mapping=NULL, linetype="dotted", linewidth = 1, ...) {
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     x <- y <- isTip <- NULL
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     dot_mapping <- aes(xend=x+diff(range(x))/200, x=max(x), yend=y, subset=isTip)
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     if (!is.null(mapping)) {
... ...
@@ -21,7 +21,7 @@ geom_aline <- function(mapping=NULL, linetype="dotted", size=1, ...) {
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     geom_segment2(dot_mapping,
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                   linetype=linetype,
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-                  size=size, stat = StatTreeData, ...)
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+                  linewidth = linewidth, stat = StatTreeData, ...)
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 }
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... ...
@@ -98,7 +98,7 @@ GeomSegmentGGtree <- ggproto("GeomSegmentGGtree", GeomSegment,
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                                  data$x <- data$x + nudge_x
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                                  data <- ggplot2::remove_missing(data, na.rm = na.rm, c("x", "y", "xend",
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-                                                        "yend", "linetype", "size", "shape"), name = "geom_segment")
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+                                                        "yend", "linetype", "linewidth", "shape"), name = "geom_segment")
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                                  if (empty(data))
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                                      return(zeroGrob())
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                                  if (!coord$is_linear()) {
... ...
@@ -123,7 +123,7 @@ GeomSegmentGGtree <- ggproto("GeomSegmentGGtree", GeomSegment,
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                                  return(grid::segmentsGrob(data$x, data$y, data$xend, data$yend,
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                                                            default.units = "native", gp = gpar(col = alpha(data$colour,
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                                                            data$alpha), fill = alpha(arrow.fill, data$alpha),
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-                                                           lwd = data$size * ggplot2::.pt, lty = data$linetype,
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+                                                           lwd = data$linewidth * ggplot2::.pt, lty = data$linetype,
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                                                            lineend = lineend, linejoin = linejoin), arrow = arrow)
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                                        )
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... ...
@@ -1,7 +1,7 @@
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 #' link between taxa 
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 #'
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 #' `geom_taxalink` supports data.frame as input,
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-#' the `colour`, `size`, `linetype` and `alpha` can be mapped. When the `data` was provided, 
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+#' the `colour`, `linewidth`, `linetype` and `alpha` can be mapped. When the `data` was provided, 
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 #' the `mapping` should be also provided, which `taxa1` and `taxa2` should be mapped created 
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 #' by `aes`, `aes_` or `aes_string`. In addition, the `hratio`, control the height of curve line, 
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 #' when tree layout is `cirular`, default is 1. `ncp`, the number of control points used to draw the 
... ...
@@ -25,7 +25,7 @@
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 #'        \item \code{group} group category of link.
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 #'        \item \code{colour} control the color of line, default is black.
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 #'        \item \code{linetype} control the type of line, default is 1 (solid).
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-#'        \item \code{size} control the width of line, default is 0.5.
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+#'        \item \code{linewidth} control the width of line, default is 0.5.
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 #'        \item \code{curvature} control the curvature of line, default is 0.5, 
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 #'        it will be created automatically in polar coordinate .
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 #'        \item \code{hratio} control the height of curve line, default is 1.
... ...
@@ -175,7 +175,8 @@ geom_curvelink <- function(data=NULL,
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 #' @importFrom scales alpha
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 GeomCurvelink <- ggproto("GeomCurvelink", GeomSegment,
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   required_aes = c("x", "y", "xend", "yend"),
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-  default_aes = aes(colour = "black", size = 0.5, linetype = 1, alpha = NA, curvature=0.5, hratio=1, ncp=1, curveangle=90, square=FALSE),
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+  default_aes = aes(colour = "black", linewidth = 0.5, linetype = 1, alpha = NA, curvature=0.5, hratio=1, ncp=1, curveangle=90, square=FALSE),
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+  rename_size = TRUE,
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   draw_panel = function(data, panel_params, coord, shape=0.5, outward=TRUE,
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                         arrow = NULL, arrow.fill=NULL, lineend = "butt", na.rm = FALSE) {
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     if (!coord$is_linear()) {
... ...
@@ -215,7 +216,7 @@ GeomCurvelink <- ggproto("GeomCurvelink", GeomSegment,
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                               square = trans$square[i], squareShape = 1, inflect = FALSE, open = TRUE,
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                               gp = gpar(col = alpha(trans$colour[i], trans$alpha[i]),
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                                         fill = alpha(arrow.fill[i], trans$alpha[i]),
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-                                        lwd = trans$size[i] * ggplot2::.pt,
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+                                        lwd = trans$linewidth[i] * ggplot2::.pt,
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                                         lty = trans$linetype[i],
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                                         lineend = lineend),
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                               arrow = arrow,
... ...
@@ -17,7 +17,7 @@
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 ##' to the left side of tip labels, defaults to "FALSE"
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 ##' with a line connecting each tip and its corresponding label, defaults to "FALSE"
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 ##' @param linetype set linetype of the line if align = TRUE, defaults to "dotted"
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-##' @param linesize set line size of the line if align = TRUE, defaults to 0.5
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+##' @param linesize set line width if align = TRUE, defaults to 0.5
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 ##' @param geom one of 'text', 'label', 'shadowtext', 'image' and 'phylopic'
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 ##' @param as_ylab display tip labels as y-axis label, 
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 ##' only works for rectangular and dendrogram layouts, defaults to "FALSE"
... ...
@@ -207,7 +207,7 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE,
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                                     "bg.colour", "bg.r"))
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     list(
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         if (show_segment){
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-            lineparams <- list(mapping = segment_mapping, linetype=linetype, nudge_x = offset, size = linesize, stat = StatTreeData)
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+            lineparams <- list(mapping = segment_mapping, linetype=linetype, nudge_x = offset, linewidth = linesize, stat = StatTreeData)
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             lineparams <- extract_params(lineparams, params, c("data", "color", "colour", "alpha", "show.legend", "na.rm",
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                                                                "inherit.aes", "arrow", "arrow.fill", "lineend")) 
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             do.call("geom_segment2", lineparams)
... ...
@@ -74,7 +74,7 @@ aesthetics are in bold):
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 \item \code{extend} extend xmax of the rectangle, defaults to 0.
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 \item \code{extendto} specify a value, meaning the rectangle extend to, defaults to NULL.
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 \item \code{linetype} the line type of margin, defaults to 1.
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-\item \code{size} the width of line of margin, defaults to 0.5.
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+\item \code{linewidth} the width of line of margin, defaults to 0.5.
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 }
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 \code{geom_hilight()} understands the following aesthethics for encircle layer (required
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 aesthetics are in bold):
... ...
@@ -85,7 +85,7 @@ aesthetics are in bold):
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 \item \code{alpha} the transparency of fill, defaults to 0.5.
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 \item \code{expand} expands the xspline clade region, defaults to 0.
87 87
 \item \code{spread} control the size, when only one point.
88
-\item \code{size} the width of line of margin, defaults to 0.5.
88
+\item \code{linewidth} the width of line of margin, defaults to 0.5.
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 \item \code{linetype} the line type of margin, defaults to 1.
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 \item \code{s_shape} the shape of the spline relative to the control points, defaults to 0.5.
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 \item \code{s_open}  whether the spline is a line or a closed shape, defaults to FALSE.
... ...
@@ -4,14 +4,14 @@
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 \alias{geom_aline}
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 \title{geom_aline}
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 \usage{
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-geom_aline(mapping = NULL, linetype = "dotted", size = 1, ...)
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+geom_aline(mapping = NULL, linetype = "dotted", linewidth = 1, ...)
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 }
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 \arguments{
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 \item{mapping}{aes mapping}
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 \item{linetype}{set line type of the line, defaults to "dotted"}
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-\item{size}{set line size of the line, defaults to 1}
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+\item{linewidth}{set width of the line, defaults to 1}
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 \item{...}{additional parameter}
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 }
... ...
@@ -11,7 +11,7 @@ geom_range(range, center = "auto", ...)
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 \item{center}{center of the range, mean, median or auto (default, the center of the range)}
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-\item{...}{additional parameter, e.g. color, size, alpha}
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+\item{...}{additional parameter, e.g. color, linewidth, alpha}
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 }
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 \value{
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 ggplot layer
... ...
@@ -36,7 +36,7 @@ a list object.
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 }
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 \description{
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 \code{geom_taxalink} supports data.frame as input,
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-the \code{colour}, \code{size}, \code{linetype} and \code{alpha} can be mapped. When the \code{data} was provided,
39
+the \code{colour}, \code{linewidth}, \code{linetype} and \code{alpha} can be mapped. When the \code{data} was provided,
40 40
 the \code{mapping} should be also provided, which \code{taxa1} and \code{taxa2} should be mapped created
41 41
 by \code{aes}, \code{aes_} or \code{aes_string}. In addition, the \code{hratio}, control the height of curve line,
42 42
 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.
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 \item \code{group} group category of link.
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 \item \code{colour} control the color of line, default is black.
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 \item \code{linetype} control the type of line, default is 1 (solid).
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-\item \code{size} control the width of line, default is 0.5.
55
+\item \code{linewidth} control the width of line, default is 0.5.
56 56
 \item \code{curvature} control the curvature of line, default is 0.5,
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 it will be created automatically in polar coordinate .
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 \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"
27 27
 
28 28
 \item{linetype}{set linetype of the line if align = TRUE, defaults to "dotted"}
29 29
 
30
-\item{linesize}{set line size of the line if align = TRUE, defaults to 0.5}
30
+\item{linesize}{set line width if align = TRUE, defaults to 0.5}
31 31
 
32 32
 \item{geom}{one of 'text', 'label', 'shadowtext', 'image' and 'phylopic'}
33 33