@@ -42,6 +42,7 @@ Suggests:

     emojifont,

     ggimage,

     ggplotify,

+    shadowtext,

     grDevices,

     knitr,

     prettydoc,

@@ -29,6 +29,7 @@ S3method(ggplot_add,hilight)

 S3method(ggplot_add,layout_ggtree)

 S3method(ggplot_add,range_xaxis)

 S3method(ggplot_add,scale_ggtree)

+S3method(ggplot_add,striplab)

 S3method(ggplot_add,striplabel)

 S3method(ggplot_add,taxalink)

 S3method(ggplot_add,tiplab)

@@ -82,6 +83,7 @@ export(geom_rootedge)

 export(geom_rootpoint)

 export(geom_segment2)

 export(geom_strip)

+export(geom_striplab)

 export(geom_taxalink)

 export(geom_text)

 export(geom_text2)

@@ -39,7 +39,7 @@

 ##' aesthetics are in bold):

 ##'     \itemize{

 ##'        \item \strong{\code{node}} selected node to hight light, it is required.

-##'        \item \strong{\code{label}} labels showed, it is required.

+##'        \item \strong{\code{label}} labels to be shown, it is required.

 ##'        \item \code{colour} the colour of text, defaults to "black".

 ##'        \item \code{size} the size of text, defaults to 3.88.

 ##'        \item \code{angle} the angle of text, defaults to 0.

@@ -58,7 +58,7 @@

 ##' aesthetics are in bold):

 ##'     \itemize{

 ##'        \item \strong{\code{node}} selected node to hight light, it is required.

-##'        \item \strong{\code{label}} labels to be showed, it is required.

+##'        \item \strong{\code{label}} labels to be shown, it is required.

 ##'        \item \code{colour} the colour of text, defaults to "black".

 ##'        \item \code{fill} the background colour of the label, defaults to "white".

 ##'        \item \code{size} the size of text, defaults to 3.88.

@@ -78,7 +78,7 @@

 ##' aesthetics are in bold):

 ##'     \itemize{

 ##'        \item \strong{\code{node}} selected node to hight light, it is required.

-##'        \item \strong{\code{label}} labels to be showed, it is required.

+##'        \item \strong{\code{label}} labels to be shown, it is required.

 ##'        \item \code{colour} the colour of text, defaults to "black".

 ##'        \item \code{bg.colour} the background colour of text, defaults to 'black'.

 ##'        \item \code{bg.r} the width of background text, defaults to 0.1.

@@ -99,7 +99,7 @@

 ##' aesthetics are in bold):

 ##'     \itemize{

 ##'        \item \strong{\code{node}} selected node to hight light, it is required.

-##'        \item \strong{\code{label}} labels to be showed, it is required.

+##'        \item \strong{\code{label}} labels to be shown, it is required.

 ##'        \item \strong{\code{image}} the image to be annotated, when geom="phylopic", 

 ##'         the uid of phylopic databases, it is required.

 ##'        \item \code{colour} the color of image, defaults to NULL.

@@ -13,6 +13,8 @@

 #' unrooted and daylight layout tree use will use encircle layer. You can specify this parameter to

 #' `rect` (rectangular layer) or `encircle` (encircle layer), 'gradient' (gradient color), 

 #' 'roundrect' (round rectangular layer).

+#' @param to.bottom logical, whether set the high light layer to the bottom in all layers of 'ggtree'

+#' object, default is FALSE.

 #' @param ... additional parameters, see also the below and Aesthetics section.

 #'     \itemize{

 #'        \item \code{align} control the align direction of the edge of high light rectangular.

@@ -82,12 +84,14 @@ geom_hilight <- function(data=NULL,

                          mapping=NULL,

                          node=NULL,

                          type="auto",

+                         to.bottom=FALSE,

                           ...){

     params <- list(...)

     structure(list(data    = data,

                    mapping = mapping,

                    node    = node,

                    type    = type,

+                   to.bottom = to.bottom,

                    params  = params),

               class = 'hilight')

 }

@@ -59,6 +59,161 @@ geom_strip <- function(taxa1, taxa2, label, offset=0, offset.text=0,

               class = "striplabel")

 }

+#' annotate associated taxa (from taxa1 to taxa2, can be Monophyletic, Polyphyletic or Paraphyletc Taxa) with bar and (optional) text label or image

+#'

+#' @title geom_striplab

+#' @param taxa1 can be label or node number

+#' @param taxa2 can be label or node number

+#' @param label character, character to be showed, when data and mapping is NULL, it is required.

+#' @param data data.frame, the data to be displayed in the annotation, default is NULL.

+#' @param mapping Set of aesthetic mappings, default is NULL. The detail see the following explanation.

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

+#' default is 'text', and the parameter see the Aesthetics For Specified Geom.

+#' @param parse logical, whether parse label to emoji font, default is FALSE.

+#' @param ... additional parameters, see also following section.

+#'

+#' additional parameters can refer the following parameters.                                                                                                                                                      ##'     \itemize{

+#'        \item \code{offset} distance bar and tree, offset of bar and text from

+#'         the clade, default is 0.

+#'        \item \code{offset.text} distance bar and text, offset of text from bar,

+#'         default is 0.

+#'        \item \code{align} logical, whether align clade lab, default is FALSE.

+#'        \item \code{extend} numeric, extend the length of bar, default is 0.

+#'        \item \code{angle} numeric or 'auto', if angle is auto, the angle of text will

+#'         be calculated automatically, which is useful for the circular etc layout, default is 0.

+#'        \item \code{horizontal} logical, whether set label to horizontal, default is TRUE.

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

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

+#'        \item \code{fontsize} the size of text, default is 3.88.

+#'        \item \code{textcolour} the colour of text, default is 'black'.

+#'        \item \code{imagesize} the size of image, default is 0.05.

+#'        \item \code{imagecolor} the colour of image, default is NULL, when

+#'        geom="phylopic", it should be required.

+#'     }

+#' The parameters also can be set in mapping, when data is provided. Note: the barsize, barcolour,

+#' fontsize, textcolour, imagesize and imagecolor should not be set in mapping (aesthetics). When

+#' the color and size are not be set in mapping, user can modify them to adjust the attributes of

+#' specified geom.

+#'

+#' @section Aesthetics For Specified Geom:

+#' \code{geom_striplab()} understands the following aesthetics for geom="text"(required

+#' aesthetics are in bold):

+#'     \itemize{

+#'        \item \strong{\code{taxa1}} selected tip label or tip node, it is required.

+#'        \item \strong{\code{taxa2}} selected another tip label or tip node, it is required.

+#'        \item \strong{\code{label}} labels to be shown, it is required.

+#'        \item \code{colour} the colour of text, default is "black".

+#'        \item \code{size} the size of text, default is 3.88.

+#'        \item \code{angle} the angle of text, default is 0.

+#'        \item \code{hjust} A numeric vector specifying horizontal justification, default is 0.

+#'        \item \code{vjust} A numeric vector specifying vertical justification, default is 0.5.

+#'        \item \code{alpha} the transparency of text, default is NA.

+#'        \item \code{family} the family of text, default is 'sans'.

+#'        \item \code{fontface} the font face of text, default is 1 (plain), others are

+#'         2 (bold), 3 (italic), 4 (bold.italic).

+#'        \item \code{lineheight} The height of a line as a multiple of the size of text, default is 1.2 .

+#'     }

+#'  when the colour, size are not be set in mapping, and user want to modify the colour of text,

+#'  they should use textcolour, fontsize to avoid the confusion with bar layer annotation.

+#'

+#' \code{geom_striplab()} understands the following aesthethics for geom="label" (required

+#' aesthetics are in bold):

+#'     \itemize{

+#'        \item \strong{\code{taxa1}} selected node to hight light, it is required.

+#'        \item \strong{\code{taxa2}} selected another tip label or tip node, it is required.

+#'        \item \strong{\code{label}} labels to be shown, it is required.

+#'        \item \code{colour} the colour of text, default is "black".

+#'        \item \code{fill} the background colour of the label, default is "white".

+#'        \item \code{size} the size of text, default is 3.88.

+#'        \item \code{angle} the angle of text, default is 0.

+#'        \item \code{hjust} A numeric vector specifying horizontal justification, default is 0.

+#'        \item \code{vjust} A numeric vector specifying vertical justification, default is 0.5.

+#'        \item \code{alpha} the transparency of text, default is NA.

+#'        \item \code{family} the family of text, default is 'sans'.

+#'        \item \code{fontface} the font face of text, default is 1 (plain), others are

+#'         2 (bold), 3 (italic), 4 (bold.italic).

+#'        \item \code{lineheight} The height of a line as a multiple of the size of text, default is 1.2 .

+#'     }

+#'  when the colour, size are not be set in mapping, and user want to modify the colour of text,

+#'  they should use textcolour, fontsize to avoid the confusion with bar layer annotation.

+#'

+#' \code{geom_striplab()} understands the following aesthethics for geom="shadowtext" (required

+#' aesthetics are in bold):

+#'     \itemize{

+#'        \item \strong{\code{taxa1}} selected node to hight light, it is required.

+#'        \item \strong{\code{taxa2}} selected another tip label or tip node, it is required.

+#'        \item \strong{\code{label}} labels to be shown, it is required.

+#'        \item \code{colour} the colour of text, default is "black".

+#'        \item \code{bg.colour} the background colour of text, default is 'black'.

+#'        \item \code{bg.r} the width of background text, default is 0.1.

+#'        \item \code{size} the size of text, default is 3.88.

+#'        \item \code{angle} the angle of text, default is 0.

+#'        \item \code{hjust} A numeric vector specifying horizontal justification, default is 0.

+#'        \item \code{vjust} A numeric vector specifying vertical justification, default is 0.5.

+#'        \item \code{alpha} the transparency of text, default is NA.

+#'        \item \code{family} the family of text, default is 'sans'.

+#'        \item \code{fontface} the font face of text, default is 1 (plain), others are

+#'         2 (bold), 3 (italic), 4 (bold.italic).

+#'        \item \code{lineheight} The height of a line as a multiple of the size of text, default is 1.2 .

+#'     }

+#'  when the colour, size are not be set in mapping, and user want to modify the colour of text,

+#'  they should use textcolour, fontsize to avoid the confusion with bar layer annotation.

+#'

+#' \code{geom_striplab()} understands the following aesthethics for geom="image" or geom="phylopic" (required

+#' aesthetics are in bold):

+#'     \itemize{

+#'        \item \strong{\code{taxa1}} selected node to hight light, it is required.

+#'        \item \strong{\code{taxa2}} selected another tip label or tip node, it is required.

+#'        \item \strong{\code{label}} labels to be shown, it is required.

+#'        \item \strong{\code{image}} the image to be annotated, when geom="phylopic",

+#'         the uid of phylopic databases, it is required.

+#'        \item \code{colour} the color of image, default is NULL.

+#'        \item \code{size} the size of image, default is 0.05.

+#'        \item \code{alpha} the alpha of image, default is 0.8.

+#'     }

+#'  when the colour, size are not be set in mapping, and user want to modify the colour of image,

+#'  they should use imagecolour, imagesize to avoid the confusion with bar layer annotation.

+#' @export

+#' @examples

+#' set.seed(123)

+#' tr <- rtree(10)

+#' dt <- data.frame(ta1=c("t5", "t1"), ta2=c("t6", "t3"), group=c("A", "B"))

+#' p <- ggtree(tr) + geom_tiplab()

+#' p2 <- p + 

+#'       geom_striplab(

+#'         data = dt,

+#'         mapping = aes(taxa1 = ta1, taxa2 = ta2, 

+#'                       label = group, color=group),

+#'         align = TRUE,

+#'         show.legend = FALSE

+#'       )

+#' p2

+geom_striplab <- function(

+               taxa1 = NULL, 

+               taxa2 = NULL,

+               label = NULL,

+               data = NULL,

+               mapping = NULL,

+               geom = "text",

+               parse = FALSE,

+               ...

+    ){

+

+    params <- list(inherit.aes = FALSE, ...)

+    structure(

+       list(

+         data = data, 

+         mapping = mapping, 

+         taxa1 = taxa1,

+         taxa2 = taxa2,

+         label = label, 

+         geom = geom, 

+         parse = parse, 

+         params = params

+       ),

+       class = "striplab")

+

+}

 ## geom_strip <- function(taxa1, taxa2, label, offset=0, offset.text=0,

 ##                            align=TRUE, barsize=0.5, extend=0, fontsize=3.88,

@@ -183,6 +338,44 @@ geom_strip <- function(taxa1, taxa2, label, offset=0, offset.text=0,

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

 ##                         )

+get_striplab_position <- function(data, taxa1, taxa2, offset, angle="auto", 

+                                  align = TRUE, extend = 0, adjustRatio = 1.02, 

+                                  horizontal = TRUE){

+    df <- get_striplab_position_(data = data, taxa1 = taxa1, taxa2 = taxa2, 

+                                 angle = angle, extend = extend, horizontal = horizontal)

+    if (align){

+        mx <- max(data$x, na.rm = TRUE)

+    }else{

+        mx <- df$x

+    }

+    angle <- df$angle

+    mx <- mx * adjustRatio + offset

+    data.frame(x = mx, xend = mx, y = df$y, yend=df$yend, angle = angle)

+}

+

+get_striplab_position_ <- function(data, taxa1, taxa2, angle, extend = 0, horizontal){

+    if (length(extend) == 1) {

+        extend <- rep(extend, 2)

+    }

+

+    node1 <- taxa2node(data, taxa1)

+    node2 <- taxa2node(data, taxa2)

+

+    xx <- with(data, c(x[node == node1], x[node == node2]))

+    yy <- with(data, c(y[node == node1], y[node == node2]))

+

+    d <- data.frame(x=max(xx), y=min(yy)-extend[2], yend=max(yy)+extend[1])

+    if (missing(angle))

+        return(d)

+    if (angle == "auto") {

+        anglerange <- with(data, c(angle[node == node1], angle[node == node2]))

+        d$angle <- mean(anglerange)

+        d$angle <- adjust_cladelabel_angle(angle=d$angle, horizontal=horizontal)

+    } else {

+        d$angle <- angle

+    }

+    return(d)    

+}

 get_striplabel_position <- function(data, taxa1, taxa2, offset, align, barextend, adjustRatio) {

     df <- get_striplabel_position_(data, taxa1, taxa2, barextend)

@@ -76,6 +76,48 @@ remapping <- function(mapping, samevars){

     return(mapping)

 }

+build_striplabel_df <- function(trdf, taxa1, taxa2, label, offset, align, angle, horizontal){

+    dat <- mapply(get_striplab_position,

+                     taxa1 = taxa1,

+                     taxa2 = taxa2,

+                     offset = offset,

+                     angle = angle,

+                     align = align,

+                     horizontal = horizontal,

+                  MoreArgs = list(

+                     data = trdf,

+                     adjustRatio = 1.03

+                  ),

+                  SIMPLIFY = FALSE

+           )

+    dat <- do.call("rbind", dat)

+    dat$y <- unlist(mapply(function(x, y){mean(c(x, y))}, dat$y, dat$yend, SIMPLIFY=FALSE))

+    dat$taxa1 <- taxa1

+    dat$taxa2 <- taxa2

+    dat$label <- label

+    return(dat)

+}

+

+build_stripbar_df <- function(trdf, taxa1, taxa2, offset, align, extend){

+    dat <- mapply(get_striplab_position,

+                     taxa1 = taxa1,

+                     taxa2 = taxa2,

+                     offset = offset,

+                     align = align,

+                     extend = extend,

+                  MoreArgs = list(

+                     data = trdf,

+                     angle = 0,

+                     adjustRatio = 1.02

+                  ),

+                  SIMPLIFY = FALSE

+           )

+    dat <- do.call("rbind", dat)

+    dat$taxa1 <- taxa1

+    dat$taxa2 <- taxa2

+    return(dat)

+}

+

 build_cladelabel_df <- function(trdf, nodeids, label, offset, align, angle, horizontal){

     dat <- mapply(function(i, o, a, g, h){get_cladelabel_position(data=trdf, 

                                           node=i, 

@@ -117,6 +159,44 @@ build_cladebar_df <- function(trdf, nodeids, offset, align, extend){

 }

+#build_striplabel_df2 <- function(trdf, taxa1, taxa2, label, offset, align, angle, horizontal){

+#    dat <- mapply(get_striplab_position2,

+#                           taxa1 = taxa1,

+#                           taxa2 = taxa2,

+#                           offset = offset,

+#                           align = align,

+#                           angle = angle,

+#                           horizontal = horizontal,

+#                           MoreArgs = list(

+#                               datai = trdf,

+#                               adjustRatio = 1.2

+#                           ),

+#                  SIMPLIFY=FALSE)

+#    dat <- do.call("rbind", dat)

+#    dat$taxa1 <- taxa1

+#    dat$taxa2 <- taxa2

+#    dat$label <- label

+#    return (dat)

+#}

+#

+#build_stripbar_df2 <- function(trdf, taxa1, taxa2, offset, align){

+#    dat <- mapply(get_striplab_position_bar,

+#                    taxa1 = taxa1,

+#                    taxa2 = taxa2,

+#                    offset = offset,

+#                    align = align,

+#                  MoreArgs = list(

+#                    data = trdf,

+#                    adjustRatio = 1.1),

+#               SIMPLIFY = FALSE

+#           )

+#    dat <- do.call("rbind", dat)

+#    colnames(dat) <- c("x", "y", "xend", "yend")

+#    dat$taxa1 <- taxa1

+#    dat$taxa2 <- taxa2

+#    return(dat)

+#}

+

 build_cladelabel_df2 <- function(trdf, nodeids, label, offset, align, angle, horizontal){

     dat <- mapply(get_cladelabel2_position_label,

                            node=nodeids,

@@ -341,7 +341,7 @@ ggplot_add.cladelab <- function(object, plot, object_name){

         flagnode <- da_node_label$node[is.na(flagnode)]

         abort(paste0("ERROR: clade node id ", paste(flagnode, collapse='; ')," can not be found in tree data."))

     }

-    if (layout == "unrooted" || layout == "daylight"){

+    if (layout %in% c("unrooted", "daylight", "ape", "equal_angle")){

         textdata <- build_cladelabel_df2(trdf=plot$data,

                                          nodeids=da_node_label$node,

                                          label=da_node_label$label,

@@ -384,6 +384,9 @@ ggplot_add.cladelab <- function(object, plot, object_name){

     bar_obj$data <- bardata

     bar_default_aes <- list(barcolour="black", barcolor="black", barsize=0.5, colour="black", size=0.5, 

                             linetype=1, alpha=NA, inherit.aes=FALSE, show.legend=NA)

+    if (layout %in% c("unrooted", "daylight", "equal_angle", "ape")){

+        bar_default_aes <- c(bar_default_aes, list(curvature = .5, ncp = 5))

+    }

     bar_obj$mapping <- reset_mapping(defaultm=bar_default_aes, inputm=object$mapping)

     ifelse(is.null(bar_obj$mapping),bar_obj$mapping <- aes_(x=~x, xend=~xend, y=~y, yend=~yend),

            bar_obj$mapping <- modifyList(bar_obj$mapping, aes_(x=~x, xend=~xend, y=~y, yend=~yend)))

@@ -392,7 +395,7 @@ ggplot_add.cladelab <- function(object, plot, object_name){

                                        default_aes=bar_default_aes,

                                        params=object$params)

     bar_obj <- c(bar_obj, bar_dot_params)

-    if (layout == "unrooted" || layout == "daylight"){

+    if (layout %in% c("unrooted", "daylight", "equal_angle", "ape")){

         bar_obj <- do.call(ggplot2::geom_curve, bar_obj)

     }else{

         bar_obj <- do.call("geom_segment", bar_obj)

@@ -488,7 +491,7 @@ ggplot_add.hilight <- function(object, plot, object_name){

         flagnode <- clade_node[is.na(flagnode)]

         abort(paste0("ERROR: clade node id ", paste(flagnode, collapse='; ')," can not be found in tree data."))

     }

-    if (layout == "unrooted" || layout == "daylight"){

+    if (layout %in% c("unrooted", "daylight", "equal_angle", "ape")){

         data <- switch(object$type,

                        auto = build_cladeids_df(trdf=framedat, nodeids=clade_node),

                        rect = build_cladeids_df2(trdf=framedat, nodeids=clade_node),

@@ -515,11 +518,11 @@ ggplot_add.hilight <- function(object, plot, object_name){

     }else{

         object$data <- data

     }

-    if (layout == "unrooted" || layout == "daylight"){

+    if (layout %in% c("unrooted", "daylight", "equal_angle", "ape")){

         ly <- switch(object$type,

                      auto = choose_hilight_layer(object = object, type = "encircle"),

                      rect = choose_hilight_layer(object = object, type = "rect"),

-                     encircle = choose_hilight_layer(object = object, type="encircle"),

+                     encircle = choose_hilight_layer(object = object, type = "encircle"),

                      gradient = choose_hilight_layer(object = object, type = "gradient"),

                      roundrect = choose_hilight_layer(object = object, type = "roundrect")

                   )

@@ -532,7 +535,12 @@ ggplot_add.hilight <- function(object, plot, object_name){

                      roundrect = choose_hilight_layer(object = object, type = "roundrect")	 

                   )

     }

-    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])

+    }

+    plot    

 }

@@ -578,6 +586,125 @@ ggplot_add.striplabel <- function(object, 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){

+    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!")

+    }

+    if (!is.null(object$data)){

+        if (is.null(object$mapping) || 

+            is.null(object$mapping$taxa1) || 

+            is.null(object$mapping$taxa2) || 

+            is.null(object$mapping$label)){

+            abort("when data is provided, the mapping also should be provided, 

+                  and taxa1, taxa2, label are required aesthetics.")

+        }else{

+            if (!is.null(object$mapping$subset)){

+                object$data <- subset(object$data, eval(parse(text=quo_name(object$mapping$subset))))

+                object$mapping <- object$mapping[names(object$mapping)!="subset"]

+            }

+            da_taxa_label <- data.frame(

+                taxa1 = as.vector(object$data[[quo_name(object$mapping$taxa1)]]),

+                taxa2 = as.vector(object$data[[quo_name(object$mapping$taxa2)]]),

+                label = as.vector(object$data[[quo_name(object$mapping$label)]])

+            )

+        }

+    }else{

+        da_taxa_label <- data.frame(taxa1 = object$taxa1, taxa2 = object$taxa2, label = object$label)

+    }    

+

+    default_raw_aes <- list(offset=0, offset.text=0, align=TRUE, angle=0, extend=0, horizontal=TRUE)

+    default_raw_aes <- reset_params(defaultp=default_raw_aes, inputp=object$params, type="other")

+    bar_params <- list(barsize=0.5, barcolour = "black")

+    bar_params <- reset_params(defaultp=bar_params, inputp=object$params, type="bar")

+    text_params <- list(fontsize= 3.88, family = "sans", textcolour="black", hjust=0)

+    text_params <- reset_params(defaultp=text_params, inputp=object$params, type="text")

+    image_params <- list(imagesize=0.05, alpha=0.8, imagecolour=NULL)

+    image_params <- reset_params(defaultp=image_params, inputp=object$params, type="image")

+    da_taxa_label <- transform_df(data = da_taxa_label, object = object, default_aes = default_raw_aes)

+    object$mapping <- object$mapping[!names(object$mapping)%in%names(default_raw_aes)]

+    object$params <- object$params[!names(object$params) %in% c("angle", "size", "color", "colour", "hjust")]

+    taxa <- unique(c(da_taxa_label$taxa1, da_taxa_label$taxa2))

+    flagnode <- match(taxa, plot$data$label)

+    if (anyNA(flagnode)){

+        flagnode <- taxa[is.na(flagnode)]

+        abort(paste0("ERROR: The taxa id: ", paste(flagnode, collapse='; ')," can not be found in tree data."))

+    }

+

+    #if (layout %in% c("unrooted", "daylight", "equal_angle", "ape")){

+    #    textdata <- build_striplabel_df2(trdf = plot$data,

+    #                                     taxa1 = da_taxa_label$taxa1,

+    #                                     taxa2 = da_taxa_label$taxa2,

+    #                                     label = da_taxa_label$label,

+    #                                     offset = da_taxa_label$offset.text,

+    #                                     align = da_taxa_label$align,

+    #                                     angle = da_taxa_label$angle,

+    #                                     horizontal = da_taxa_label$horizontal)

+    #    bardata <- build_stripbar_df2(trdf = plot$data,

+    #                                  taxa1 = da_taxa_label$taxa1,

+    #                                  taxa2 = da_taxa_label$taxa2,

+    #                                  offset = da_taxa_label$offset,

+    #                                  align = da_taxa_label$align)

+    #}else{

+    textdata <- build_striplabel_df(trdf = plot$data,

+                                    taxa1 = da_taxa_label$taxa1,

+                                    taxa2 = da_taxa_label$taxa2,

+                                    label = da_taxa_label$label,

+                                    offset = da_taxa_label$offset.text,

+                                    align = da_taxa_label$align,

+                                    angle = da_taxa_label$angle,

+                                    horizontal = da_taxa_label$horizontal)

+    bardata <- build_stripbar_df(trdf = plot$data,

+                                 taxa1 = da_taxa_label$taxa1,

+                                 taxa2 = da_taxa_label$taxa2,

+                                 offset = da_taxa_label$offset,

+                                 align = da_taxa_label$align,

+                                 extend = da_taxa_label$extend)

+    #}

+

+    if (!is.null(object$data) && !is.null(object$mapping)){

+        object$data <- object$data[,!colnames(object$data) %in% c("x", "xend", "y", "yend", "label", "angle"),drop=FALSE]

+        textdata <- dplyr::left_join(textdata, object$data, 

+                                     by=c("taxa1"=quo_name(object$mapping$taxa1), 

+                                          "taxa2"=quo_name(object$mapping$taxa2))

+                    )

+        bardata <- dplyr::left_join(bardata, 

+                                    object$data, 

+                                    by=c("taxa1"=quo_name(object$mapping$taxa1), 

+                                         "taxa2"=quo_name(object$mapping$taxa2))

+                    )

+        object$mapping <- object$mapping[!names(object$mapping) %in% c("taxa1", "taxa2", "node", "label")]

+    }

+    annot_obj <- switch(object$geom,

+                        text = build_text_layer(data=textdata, object=object, params=text_params, layout=layout),

+                        label = build_text_layer(data=textdata, object=object, params=text_params, layout=layout),

+                        image = build_image_layer(data=textdata, object=object, params=image_params),

+                        phylopic = build_image_layer(data=textdata, object=object, params=image_params),

+                        shadowtext = build_text_layer(data=textdata, object=object, params=text_params),

+                       )

+    bar_obj <- list()

+    bar_obj$data <- bardata

+    bar_default_aes <- list(barcolour="black", barcolor="black", barsize=0.5, colour="black", size=0.5,

+                            linetype=1, alpha=NA, inherit.aes=FALSE, show.legend=NA)

+    bar_obj$mapping <- reset_mapping(defaultm=bar_default_aes, inputm=object$mapping)

+    ifelse(is.null(bar_obj$mapping),bar_obj$mapping <- aes_(x=~x, xend=~xend, y=~y, yend=~yend),

+           bar_obj$mapping <- modifyList(bar_obj$mapping, aes_(x=~x, xend=~xend, y=~y, yend=~yend)))

+    bar_dot_params <- reset_dot_params(mapping=bar_obj$mapping,

+                                       defaultp=bar_params,

+                                       default_aes=bar_default_aes,

+                                       params=object$params)

+    bar_obj <- c(bar_obj, bar_dot_params)

+    #if (layout %in% c("unrooted", "daylight", "ape", "equal_angle")){

+    #    bar_obj <- do.call(ggplot2::geom_curve, bar_obj)

+    #}else{

+    bar_obj <- do.call("geom_segment", bar_obj)

+    #}

+    obj <- list(annot_obj, bar_obj)

+    ggplot_add(obj, plot, object_name)

+}

+

 ##' @importFrom ggplot2 scale_x_continuous

 ##' @importFrom ggplot2 scale_x_date

 ##' @method ggplot_add scale_ggtree

@@ -5,9 +5,23 @@

 \alias{geom_highlight}

 \title{geom_hilight}

 \usage{

-geom_hilight(data = NULL, mapping = NULL, node = NULL, type = "auto", ...)

+geom_hilight(

+  data = NULL,

+  mapping = NULL,

+  node = NULL,

+  type = "auto",

+  to.bottom = FALSE,

+  ...

+)

-geom_highlight(data = NULL, mapping = NULL, node = NULL, type = "auto", ...)

+geom_highlight(

+  data = NULL,

+  mapping = NULL,

+  node = NULL,

+  type = "auto",

+  to.bottom = FALSE,

+  ...

+)

 }

 \arguments{

 \item{data}{data.frame, The data to be displayed in this layer, defaults to NULL.}

@@ -22,6 +36,9 @@ unrooted and daylight layout tree use will use encircle layer. You can specify t

 \code{rect} (rectangular layer) or \code{encircle} (encircle layer), 'gradient' (gradient color),

 'roundrect' (round rectangular layer).}

+\item{to.bottom}{logical, whether set the high light layer to the bottom in all layers of 'ggtree'

+object, default is FALSE.}

+

 \item{...}{additional parameters, see also the below and Aesthetics section.

 \itemize{

 \item \code{align} control the align direction of the edge of high light rectangular.

@@ -63,7 +63,7 @@ annotate a clade with bar and text label or (image)

 aesthetics are in bold):

 \itemize{

 \item \strong{\code{node}} selected node to hight light, it is required.

-\item \strong{\code{label}} labels showed, it is required.

+\item \strong{\code{label}} labels to be shown, it is required.

 \item \code{colour} the colour of text, defaults to "black".

 \item \code{size} the size of text, defaults to 3.88.

 \item \code{angle} the angle of text, defaults to 0.

@@ -82,7 +82,7 @@ they should use textcolour, fontsize to avoid the confusion with bar layer annot

 aesthetics are in bold):

 \itemize{

 \item \strong{\code{node}} selected node to hight light, it is required.

-\item \strong{\code{label}} labels to be showed, it is required.

+\item \strong{\code{label}} labels to be shown, it is required.

 \item \code{colour} the colour of text, defaults to "black".

 \item \code{fill} the background colour of the label, defaults to "white".

 \item \code{size} the size of text, defaults to 3.88.

@@ -102,7 +102,7 @@ they should use textcolour, fontsize to avoid the confusion with bar layer annot

 aesthetics are in bold):

 \itemize{

 \item \strong{\code{node}} selected node to hight light, it is required.

-\item \strong{\code{label}} labels to be showed, it is required.

+\item \strong{\code{label}} labels to be shown, it is required.

 \item \code{colour} the colour of text, defaults to "black".

 \item \code{bg.colour} the background colour of text, defaults to 'black'.

 \item \code{bg.r} the width of background text, defaults to 0.1.

@@ -123,7 +123,7 @@ they should use textcolour, fontsize to avoid the confusion with bar layer annot

 aesthetics are in bold):

 \itemize{

 \item \strong{\code{node}} selected node to hight light, it is required.

-\item \strong{\code{label}} labels to be showed, it is required.

+\item \strong{\code{label}} labels to be shown, it is required.

 \item \strong{\code{image}} the image to be annotated, when geom="phylopic",

 the uid of phylopic databases, it is required.

 \item \code{colour} the color of image, defaults to NULL.

new file mode 100644

@@ -0,0 +1,157 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/geom_strip.R

+\name{geom_striplab}

+\alias{geom_striplab}

+\title{geom_striplab}

+\usage{

+geom_striplab(

+  taxa1 = NULL,

+  taxa2 = NULL,

+  label = NULL,

+  data = NULL,

+  mapping = NULL,

+  geom = "text",

+  parse = FALSE,

+  ...

+)

+}

+\arguments{

+\item{taxa1}{can be label or node number}

+

+\item{taxa2}{can be label or node number}

+

+\item{label}{character, character to be showed, when data and mapping is NULL, it is required.}

+

+\item{data}{data.frame, the data to be displayed in the annotation, default is NULL.}

+

+\item{mapping}{Set of aesthetic mappings, default is NULL. The detail see the following explanation.}

+

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

+default is 'text', and the parameter see the Aesthetics For Specified Geom.}

+

+\item{parse}{logical, whether parse label to emoji font, default is FALSE.}

+

+\item{...}{additional parameters, see also following section.

+

+additional parameters can refer the following parameters.                                                                                                                                                      ##'     \itemize{

+\item \code{offset} distance bar and tree, offset of bar and text from

+the clade, default is 0.

+\item \code{offset.text} distance bar and text, offset of text from bar,

+default is 0.

+\item \code{align} logical, whether align clade lab, default is FALSE.

+\item \code{extend} numeric, extend the length of bar, default is 0.

+\item \code{angle} numeric or 'auto', if angle is auto, the angle of text will

+be calculated automatically, which is useful for the circular etc layout, default is 0.

+\item \code{horizontal} logical, whether set label to horizontal, default is TRUE.

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

+\item \code{barcolour} the colour of line, default is 'black'.

+\item \code{fontsize} the size of text, default is 3.88.

+\item \code{textcolour} the colour of text, default is 'black'.

+\item \code{imagesize} the size of image, default is 0.05.

+\item \code{imagecolor} the colour of image, default is NULL, when

+geom="phylopic", it should be required.

+}

+The parameters also can be set in mapping, when data is provided. Note: the barsize, barcolour,

+fontsize, textcolour, imagesize and imagecolor should not be set in mapping (aesthetics). When

+the color and size are not be set in mapping, user can modify them to adjust the attributes of

+specified geom.}

+}

+\description{

+annotate associated taxa (from taxa1 to taxa2, can be Monophyletic, Polyphyletic or Paraphyletc Taxa) with bar and (optional) text label or image

+}

+\section{Aesthetics For Specified Geom}{

+

+\code{geom_striplab()} understands the following aesthetics for geom="text"(required

+aesthetics are in bold):

+\itemize{

+\item \strong{\code{taxa1}} selected tip label or tip node, it is required.

+\item \strong{\code{taxa2}} selected another tip label or tip node, it is required.

+\item \strong{\code{label}} labels to be shown, it is required.

+\item \code{colour} the colour of text, default is "black".

+\item \code{size} the size of text, default is 3.88.

+\item \code{angle} the angle of text, default is 0.

+\item \code{hjust} A numeric vector specifying horizontal justification, default is 0.

+\item \code{vjust} A numeric vector specifying vertical justification, default is 0.5.

+\item \code{alpha} the transparency of text, default is NA.

+\item \code{family} the family of text, default is 'sans'.

+\item \code{fontface} the font face of text, default is 1 (plain), others are

+2 (bold), 3 (italic), 4 (bold.italic).

+\item \code{lineheight} The height of a line as a multiple of the size of text, default is 1.2 .

+}

+when the colour, size are not be set in mapping, and user want to modify the colour of text,

+they should use textcolour, fontsize to avoid the confusion with bar layer annotation.

+

+\code{geom_striplab()} understands the following aesthethics for geom="label" (required

+aesthetics are in bold):

+\itemize{

+\item \strong{\code{taxa1}} selected node to hight light, it is required.

+\item \strong{\code{taxa2}} selected another tip label or tip node, it is required.

+\item \strong{\code{label}} labels to be shown, it is required.

+\item \code{colour} the colour of text, default is "black".

+\item \code{fill} the background colour of the label, default is "white".

+\item \code{size} the size of text, default is 3.88.

+\item \code{angle} the angle of text, default is 0.

+\item \code{hjust} A numeric vector specifying horizontal justification, default is 0.

+\item \code{vjust} A numeric vector specifying vertical justification, default is 0.5.

+\item \code{alpha} the transparency of text, default is NA.

+\item \code{family} the family of text, default is 'sans'.

+\item \code{fontface} the font face of text, default is 1 (plain), others are

+2 (bold), 3 (italic), 4 (bold.italic).

+\item \code{lineheight} The height of a line as a multiple of the size of text, default is 1.2 .

+}

+when the colour, size are not be set in mapping, and user want to modify the colour of text,

+they should use textcolour, fontsize to avoid the confusion with bar layer annotation.

+

+\code{geom_striplab()} understands the following aesthethics for geom="shadowtext" (required

+aesthetics are in bold):

+\itemize{

+\item \strong{\code{taxa1}} selected node to hight light, it is required.

+\item \strong{\code{taxa2}} selected another tip label or tip node, it is required.

+\item \strong{\code{label}} labels to be shown, it is required.

+\item \code{colour} the colour of text, default is "black".

+\item \code{bg.colour} the background colour of text, default is 'black'.

+\item \code{bg.r} the width of background text, default is 0.1.

+\item \code{size} the size of text, default is 3.88.

+\item \code{angle} the angle of text, default is 0.

+\item \code{hjust} A numeric vector specifying horizontal justification, default is 0.

+\item \code{vjust} A numeric vector specifying vertical justification, default is 0.5.

+\item \code{alpha} the transparency of text, default is NA.

+\item \code{family} the family of text, default is 'sans'.

+\item \code{fontface} the font face of text, default is 1 (plain), others are

+2 (bold), 3 (italic), 4 (bold.italic).

+\item \code{lineheight} The height of a line as a multiple of the size of text, default is 1.2 .

+}

+when the colour, size are not be set in mapping, and user want to modify the colour of text,

+they should use textcolour, fontsize to avoid the confusion with bar layer annotation.

+

+\code{geom_striplab()} understands the following aesthethics for geom="image" or geom="phylopic" (required

+aesthetics are in bold):

+\itemize{

+\item \strong{\code{taxa1}} selected node to hight light, it is required.

+\item \strong{\code{taxa2}} selected another tip label or tip node, it is required.

+\item \strong{\code{label}} labels to be shown, it is required.

+\item \strong{\code{image}} the image to be annotated, when geom="phylopic",

+the uid of phylopic databases, it is required.

+\item \code{colour} the color of image, default is NULL.

+\item \code{size} the size of image, default is 0.05.

+\item \code{alpha} the alpha of image, default is 0.8.

+}

+when the colour, size are not be set in mapping, and user want to modify the colour of image,

+they should use imagecolour, imagesize to avoid the confusion with bar layer annotation.

+}

+

+\examples{

+set.seed(123)

+tr <- rtree(10)

+dt <- data.frame(ta1=c("t5", "t1"), ta2=c("t6", "t3"), group=c("A", "B"))

+p <- ggtree(tr) + geom_tiplab()

+p2 <- p + 

+      geom_striplab(

+        data = dt,

+        mapping = aes(taxa1 = ta1, taxa2 = ta2, 

+                      label = group, color=group),

+        align = TRUE,

+        show.legend = FALSE

+      )

+p2

+}