@@ -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)

@@ -4,24 +4,34 @@

 ##' @title geom_strip

 ##' @param taxa1 taxa1

 ##' @param taxa2 taxa2

-##' @param label optional label

+##' @param label add label alongside the bar (optional)

 ##' @param offset offset of bar and text from the clade

 ##' @param offset.text offset of text from bar

-##' @param align logical

-##' @param barsize size of bar

-##' @param extend extend bar vertically

-##' @param fontsize size of text

-##' @param angle angle of text

+##' @param align logical, whether to align bars to the most distant bar ,defaults to "TRUE"

+##' Note that if "FALSE", the bars might cross the tree

+##' @param barsize set size of the bar

+##' @param extend extend bar length vertically

+##' @param fontsize set size of the text

+##' @param angle set the angle of text

 ##' @param geom one of 'text' or 'label'

-##' @param hjust hjust

-##' @param color color for bar and label

-##' @param fill fill label background, only work with geom='label'

-##' @param family sans by default, can be any supported font

-##' @param parse logical, whether parse label

+##' @param hjust adjust the horizonal position of the bar

+##' @param color set color for bar and label

+##' @param fill set color to fill label background, only work with geom='label'

+##' @param family "sans" by default, can be any supported font

+##' @param parse logical, whether to parse labels, if "TRUE", the labels will be parsed into expressions, defaults to "FALSE"

 ##' @param ... additional parameter

 ##' @return ggplot layers

 ##' @export

 ##' @author Guangchuang Yu

+##' @examples

+##' library(ggtree)

+##' tr<- rtree(15)

+##' x <- ggtree(tr)

+##' x + geom_strip(13, 1, color = "red") + geom_strip(3, 7, color = "blue")

+##' @references

+##' For more detailed demonstration of this function, please refer to chapter 5.2.1 of 

+##' *Data Integration, Manipulation and Visualization of Phylogenetic Trees*

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

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

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

                        angle=0, geom="text", hjust=0, color = 'black', fill=NA, family="sans",

@@ -14,6 +14,7 @@

 ##' @param angle angle of text

 ##' @param geom one of 'text' or 'label'

 ##' @param hjust hjust

+##' @param color color for bar and label

 ##' @param fill fill label background, only work with geom='label'

 ##' @param family sans by default, can be any supported font

 ##' @param parse logical, whether parse label

@@ -23,7 +24,7 @@

 ##' @author Guangchuang Yu

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

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

-                       angle=0, geom="text", hjust=0, fill=NA, family="sans",

+                       angle=0, geom="text", hjust=0, color = 'black', fill=NA, family="sans",

                        parse=FALSE, ...) {

     if (missing(label)) label <- NA

@@ -40,6 +41,7 @@ geom_strip <- function(taxa1, taxa2, label, offset=0, offset.text=0,

                    angle = angle,

                    geom = geom,

                    hjust = hjust,

+                   color = color,

                    fill = fill,

                    family = family,

                    parse = parse,

@@ -21,144 +21,155 @@

 ##' @return ggplot layers

 ##' @export

 ##' @author Guangchuang Yu

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

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

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

                        angle=0, geom="text", hjust=0, fill=NA, family="sans",

                        parse=FALSE, ...) {

-    mapping <- NULL

-    data <- NULL

-    position <- "identity"

-    show.legend <- NA

-    na.rm <- TRUE

-    inherit.aes <- FALSE

-

-    layer_bar <- stat_stripBar(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset, align=align,

-                               size=barsize, barextend=extend,

-                               mapping=mapping, data=data,

-                               position=position, show.legend = show.legend,

-                               inherit.aes = inherit.aes, na.rm=na.rm, ...)

-

-    if (is.na(label) || is.null(label)) {

-        return(layer_bar)

-    }

-

-    if (geom == "text") {

-        ## no fill parameter

-        layer_text <- stat_stripText(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset+offset.text,

-                                    align=align, size=fontsize, barextend=extend, angle=angle, family=family,

-                                    mapping=mapping, data=data, geom=geom, hjust=hjust,

-                                    position=position, show.legend = show.legend,

-                                    inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...)

-

-    } else {

-        layer_text <- stat_stripText(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset+offset.text,

-                                    align=align, size=fontsize, barextend=extend, angle=angle, fill=fill,family=family,

-                                    mapping=mapping, data=data, geom=geom, hjust=hjust,

-                                    position=position, show.legend = show.legend,

-                                    inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...)

-    }

-    list(

-        layer_bar,

-        layer_text

-    )

+    if (missing(label)) label <- NA

+

+    structure(list(taxa1 = taxa1,

+                   taxa2 = taxa2,

+                   label = label,

+                   offset = offset,

+                   offset.text = offset.text,

+                   align = align,

+                   barsize = barsize,

+                   extend = extend,

+                   fontsize = fontsize,

+                   angle = angle,

+                   geom = geom,

+                   hjust = hjust,

+                   fill = fill,

+                   family = family,

+                   parse = parse,

+                   params = list(...)),

+              class = "striplabel")

 }

-stat_stripText <- function(mapping=NULL, data=NULL,

-                           geom="text", position="identity",

-                           taxa1, taxa2, label, offset, align, barextend, ...,

-                           show.legend=NA, inherit.aes=FALSE, na.rm=FALSE, parse=FALSE) {

-

-    if (is.null(label) || is.na(label)) {

-        default_aes <- aes_(x=~x, y=~y, node=~node, label=~label)

-    } else {

-        default_aes <- aes_(x=~x, y=~y, node=~node)

-    }

-

-    if (is.null(mapping)) {

-        mapping <- default_aes

-    } else {

-        mapping <- modifyList(mapping, default_aes)

-    }

-

-    layer(stat=StatStripText,

-          data=data,

-          mapping=mapping,

-          geom=geom,

-          position=position,

-          show.legend = show.legend,

-          inherit.aes = inherit.aes,

-          params=list(taxa1=taxa1,

-                      taxa2=taxa2,

-                      label=label,

-                      offset=offset,

-                      align=align,

-                      barextend=barextend,

-                      na.rm=na.rm,

-                      parse=parse,

-                      ...),

-          check.aes = FALSE

-          )

-

-}

-

-stat_stripBar <- function(mapping=NULL, data=NULL,

-                          geom="segment", position="identity",

-                          taxa1, taxa2, label=label, offset, align, barextend, ...,

-                          show.legend=NA, inherit.aes=FALSE, na.rm=FALSE) {

-

-    if (is.null(label) || is.na(label)) {

-        default_aes <- aes_(x=~x, y=~y, node=~node, label=~label, xend=~x, yend=~y)

-    } else {

-        default_aes <- aes_(x=~x, y=~y, node=~node, xend=~x, yend=~y)

-    }

-

-    if (is.null(mapping)) {

-        mapping <- default_aes

-    } else {

-        mapping <- modifyList(mapping, default_aes)

-    }

-

-    layer(stat=StatStripBar,

-          data=data,

-          mapping=mapping,

-          geom=geom,

-          position=position,

-          show.legend = show.legend,

-          inherit.aes = inherit.aes,

-          params=list(taxa1=taxa1,

-                      taxa2=taxa2,

-                      offset=offset,

-                      align=align,

-                      barextend=barextend,

-                      na.rm=na.rm,

-                      ...),

-          check.aes = FALSE

-          )

-

-}

-

-StatStripText <- ggproto("StatStripText", Stat,

-                         compute_group = function(self, data, scales, params, taxa1, taxa2,

-                                                  label, offset, align, barextend) {

-                             df <- get_striplabel_position(data, taxa1, taxa2, offset, align, barextend, adjustRatio = 1.03)

-                             df$y <- mean(c(df$y, df$yend))

-                             df$label <- label

-                             return(df)

-                         },

-                         required_aes = c("x", "y", "label")

-                         )

-

-

-

-StatStripBar <- ggproto("StatStripBar", Stat,

-                        compute_group = function(self, data, scales, params,

-                                                 taxa1, taxa2, offset, align, barextend) {

-                            get_striplabel_position(data, taxa1, taxa2, offset, align, barextend, adjustRatio=1.02)

-                        },

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

-                        )

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

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

+##                            angle=0, geom="text", hjust=0, fill=NA, family="sans",

+##                            parse=FALSE, ...) {

+

+##     mapping <- aes_(x=~x, y=~y, node=~node, label = ~label, xend=~x, yend=~y)

+##     data <- NULL

+##     position <- "identity"

+##     show.legend <- NA

+##     na.rm <- TRUE

+##     inherit.aes <- FALSE

+

+##     layer_bar <- stat_stripBar(taxa1=taxa1, taxa2=taxa2, offset=offset, align=align,

+##                                size=barsize, barextend=extend,

+##                                mapping=mapping, data=data,

+##                                position=position, show.legend = show.legend,

+##                                inherit.aes = inherit.aes, na.rm=na.rm, ...)

+

+##     if (missing(label) || is.na(label) || is.null(label)) {

+##         return(layer_bar)

+##     }

+

+##     if (geom == "text") {

+##         ## no fill parameter

+##         layer_text <- stat_stripText(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset+offset.text,

+##                                      align=align, size=fontsize, barextend=extend, angle=angle, family=family,

+##                                      mapping=mapping, data=data, geom=geom, hjust=hjust,

+##                                      position=position, show.legend = show.legend,

+##                                      inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...)

+

+##     } else {

+##         layer_text <- stat_stripText(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset+offset.text,

+##                                      align=align, size=fontsize, barextend=extend, angle=angle,

+##                                      fill=fill,family=family,

+##                                      mapping=mapping, data=data, geom=geom, hjust=hjust,

+##                                      position=position, show.legend = show.legend,

+##                                      inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...)

+##     }

+

+##     list(

+##         layer_bar,

+##         layer_text

+##     )

+## }

+

+

+## stat_stripText <- function(mapping=NULL, data=NULL,

+##                            geom="text", position="identity",

+##                            taxa1, taxa2, label, offset, align, barextend, ...,

+##                            show.legend=NA, inherit.aes=FALSE, na.rm=FALSE, parse=FALSE) {

+

+##     layer(stat=StatStripText,

+##           data=data,

+##           mapping=mapping,

+##           geom=geom,

+##           position=position,

+##           show.legend = show.legend,

+##           inherit.aes = inherit.aes,

+##           params=list(taxa1=taxa1,

+##                       taxa2=taxa2,

+##                       label=label,

+##                       offset=offset,

+##                       align=align,

+##                       barextend=barextend,

+##                       na.rm=na.rm,

+##                       parse=parse,

+##                       ...),

+##           check.aes = FALSE

+##           )

+

+## }

+

+## stat_stripBar <- function(mapping=NULL, data=NULL,

+##                           geom="segment", position="identity",

+##                           taxa1, taxa2, offset, align, barextend, ...,

+##                           show.legend=NA, inherit.aes=FALSE, na.rm=FALSE) {

+

+##     layer(stat=StatStripBar,

+##           data=data,

+##           mapping=mapping,

+##           geom=geom,

+##           position=position,

+##           show.legend = show.legend,

+##           inherit.aes = inherit.aes,

+##           params=list(taxa1=taxa1,

+##                       taxa2=taxa2,

+##                       offset=offset,

+##                       align=align,

+##                       barextend=barextend,

+##                       na.rm=na.rm,

+##                       ...),

+##           check.aes = FALSE

+##           )

+

+## }

+

+## StatStripText <- ggproto("StatStripText", Stat,

+##                          compute_group = function(self, data, scales, params, taxa1, taxa2,

+##                                                   label, offset, align, barextend) {

+##                              print('text' )

+##                              print(data )

+##                              df <- get_striplabel_position(data, taxa1, taxa2, offset, align,

+##                                                            barextend, adjustRatio = 1.03)

+##                              df$y <- mean(c(df$y, df$yend))

+##                              df$label <- label

+##                              return(df)

+##                          },

+##                          required_aes = c("x", "y", "label")

+##                          )

+

+

+

+## StatStripBar <- ggproto("StatStripBar", Stat,

+##                         compute_group = function(self, data, scales, params,

+##                                                  taxa1, taxa2, offset, align, barextend) {

+##                             print('bar' )

+##                             print(data )

+##                             get_striplabel_position(data, taxa1, taxa2, offset,

+##                                                     align, barextend, adjustRatio=1.02)

+##                         },

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

+##                         )

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

@@ -177,6 +188,7 @@ get_striplabel_position_ <- function(data, taxa1, taxa2, barextend=0) {

     if (length(barextend) == 1) {

         barextend <- rep(barextend, 2)

     }

+

     node1 <- taxa2node(data, taxa1)

     node2 <- taxa2node(data, taxa2)

@@ -188,15 +200,21 @@ get_striplabel_position_ <- function(data, taxa1, taxa2, barextend=0) {

 ## used in geom_strip, geom_taxalink

 taxa2node <- function(data, taxa) {

-    if (! 'label' %in% colnames(data))

-        data$label <- NA

+    ## if (! 'label' %in% colnames(data))

+    ##     data$label <- NA

-    idx <- with(data, which(taxa == label | taxa == node))

+    ## idx <- which(taxa == data$label | taxa == data$node)

-    if (length(idx) == 0) {

-        stop("input taxa is not valid...")

-    }

+    ## if (length(idx) == 0) {

+    ##     print(taxa )

+    ##     print(data )

+    ##     stop("input taxa is not valid...")

+    ## }

+

+    ## return(data$node[idx])

+    if (is.numeric(taxa))

+        return(taxa)

-    return(data$node[idx])

+    nodeid.tbl_tree(data, taxa)

 }

@@ -9,7 +9,7 @@

 ##' @param offset.text offset of text from bar

 ##' @param align logical

 ##' @param barsize size of bar

-##' @param barextend extend bar vertically

+##' @param extend extend bar vertically

 ##' @param fontsize size of text

 ##' @param angle angle of text

 ##' @param geom one of 'text' or 'label'

@@ -22,7 +22,7 @@

 ##' @export

 ##' @author Guangchuang Yu

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

-                       align=TRUE, barsize=0.5, barextend=0, fontsize=3.88,

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

                        angle=0, geom="text", hjust=0, fill=NA, family="sans",

                        parse=FALSE, ...) {

     mapping <- NULL

@@ -33,7 +33,7 @@ geom_strip <- function(taxa1, taxa2, label=NA, offset=0, offset.text=0,

     inherit.aes <- FALSE

     layer_bar <- stat_stripBar(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset, align=align,

-                               size=barsize, barextend=barextend,

+                               size=barsize, barextend=extend,

                                mapping=mapping, data=data,

                                position=position, show.legend = show.legend,

                                inherit.aes = inherit.aes, na.rm=na.rm, ...)

@@ -45,14 +45,14 @@ geom_strip <- function(taxa1, taxa2, label=NA, offset=0, offset.text=0,

     if (geom == "text") {

         ## no fill parameter

         layer_text <- stat_stripText(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset+offset.text,

-                                    align=align, size=fontsize, barextend=barextend, angle=angle, family=family,

+                                    align=align, size=fontsize, barextend=extend, angle=angle, family=family,

                                     mapping=mapping, data=data, geom=geom, hjust=hjust,

                                     position=position, show.legend = show.legend,

                                     inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...)

     } else {

         layer_text <- stat_stripText(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset+offset.text,

-                                    align=align, size=fontsize, barextend=barextend, angle=angle, fill=fill,family=family,

+                                    align=align, size=fontsize, barextend=extend, angle=angle, fill=fill,family=family,

                                     mapping=mapping, data=data, geom=geom, hjust=hjust,

                                     position=position, show.legend = show.legend,

                                     inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...)

@@ -174,13 +174,16 @@ get_striplabel_position <- function(data, taxa1, taxa2, offset, align, barextend

 get_striplabel_position_ <- function(data, taxa1, taxa2, barextend=0) {

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

+        barextend <- rep(barextend, 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]))

-    data.frame(x=max(xx), y=min(yy)-barextend, yend=max(yy)+barextend)

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

 }

 ## used in geom_strip, geom_taxalink

@@ -98,7 +98,7 @@ stat_stripText <- function(mapping=NULL, data=NULL,

                       na.rm=na.rm,

                       parse=parse,

                       ...),

-          if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE

+          check.aes = FALSE

           )

 }

@@ -134,7 +134,7 @@ stat_stripBar <- function(mapping=NULL, data=NULL,

                       barextend=barextend,

                       na.rm=na.rm,

                       ...),

-          if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE

+          check.aes = FALSE

           )

 }

@@ -1,6 +1,6 @@

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

 ##'

-##' 

+##'

 ##' @title geom_strip

 ##' @param taxa1 taxa1

 ##' @param taxa2 taxa2

@@ -34,14 +34,14 @@ geom_strip <- function(taxa1, taxa2, label=NA, offset=0, offset.text=0,

     layer_bar <- stat_stripBar(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset, align=align,

                                size=barsize, barextend=barextend,

-                               mapping=mapping, data=data, 

+                               mapping=mapping, data=data,

                                position=position, show.legend = show.legend,

                                inherit.aes = inherit.aes, na.rm=na.rm, ...)

     if (is.na(label) || is.null(label)) {

         return(layer_bar)

     }

-    

+

     if (geom == "text") {

         ## no fill parameter

         layer_text <- stat_stripText(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset+offset.text,

@@ -49,7 +49,7 @@ geom_strip <- function(taxa1, taxa2, label=NA, offset=0, offset.text=0,

                                     mapping=mapping, data=data, geom=geom, hjust=hjust,

                                     position=position, show.legend = show.legend,

                                     inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...)

-        

+

     } else {

         layer_text <- stat_stripText(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset+offset.text,

                                     align=align, size=fontsize, barextend=barextend, angle=angle, fill=fill,family=family,

@@ -57,7 +57,7 @@ geom_strip <- function(taxa1, taxa2, label=NA, offset=0, offset.text=0,

                                     position=position, show.legend = show.legend,

                                     inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...)

     }

-    

+

     list(

         layer_bar,

         layer_text

@@ -75,13 +75,13 @@ stat_stripText <- function(mapping=NULL, data=NULL,

     } else {

         default_aes <- aes_(x=~x, y=~y, node=~node)

     }

-    

+

     if (is.null(mapping)) {

         mapping <- default_aes

     } else {

         mapping <- modifyList(mapping, default_aes)

     }

-    

+

     layer(stat=StatStripText,

           data=data,

           mapping=mapping,

@@ -100,7 +100,7 @@ stat_stripText <- function(mapping=NULL, data=NULL,

                       ...),

           if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE

           )

-    

+

 }

 stat_stripBar <- function(mapping=NULL, data=NULL,

@@ -111,7 +111,7 @@ stat_stripBar <- function(mapping=NULL, data=NULL,

     if (is.null(label) || is.na(label)) {

         default_aes <- aes_(x=~x, y=~y, node=~node, label=~label, xend=~x, yend=~y)

     } else {

-        default_aes <- aes_(x=~x, y=~y, node=~node)

+        default_aes <- aes_(x=~x, y=~y, node=~node, xend=~x, yend=~y)

     }

     if (is.null(mapping)) {

@@ -119,7 +119,7 @@ stat_stripBar <- function(mapping=NULL, data=NULL,

     } else {

         mapping <- modifyList(mapping, default_aes)

     }

-    

+

     layer(stat=StatStripBar,

           data=data,

           mapping=mapping,

@@ -150,8 +150,8 @@ StatStripText <- ggproto("StatStripText", Stat,

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

                          )

-                         

-                          

+

+

 StatStripBar <- ggproto("StatStripBar", Stat,

                         compute_group = function(self, data, scales, params,

                                                  taxa1, taxa2, offset, align, barextend) {

@@ -193,7 +193,7 @@ taxa2node <- function(data, taxa) {

     if (length(idx) == 0) {

         stop("input taxa is not valid...")

     }

-    

+

     return(data$node[idx])

 }

@@ -98,7 +98,7 @@ stat_stripText <- function(mapping=NULL, data=NULL,

                       na.rm=na.rm,

                       parse=parse,

                       ...),

-          check.aes = FALSE

+          if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE

           )

 }

@@ -134,7 +134,7 @@ stat_stripBar <- function(mapping=NULL, data=NULL,

                       barextend=barextend,

                       na.rm=na.rm,

                       ...),

-          check.aes = FALSE

+          if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE

           )

 }

@@ -97,7 +97,8 @@ stat_stripText <- function(mapping=NULL, data=NULL,

                       barextend=barextend,

                       na.rm=na.rm,

                       parse=parse,

-                      ...)

+                      ...),

+          check.aes = FALSE

           )

 }

@@ -132,7 +133,8 @@ stat_stripBar <- function(mapping=NULL, data=NULL,

                       align=align,

                       barextend=barextend,

                       na.rm=na.rm,

-                      ...)

+                      ...),

+          check.aes = FALSE

           )

 }

@@ -16,13 +16,15 @@

 ##' @param hjust hjust

 ##' @param fill fill label background, only work with geom='label'

 ##' @param family sans by default, can be any supported font

+##' @param parse logical, whether parse label

 ##' @param ... additional parameter

 ##' @return ggplot layers

 ##' @export

 ##' @author Guangchuang Yu

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

                        align=TRUE, barsize=0.5, barextend=0, fontsize=3.88,

-                       angle=0, geom="text", hjust=0, fill=NA, family="sans", ...) {

+                       angle=0, geom="text", hjust=0, fill=NA, family="sans",

+                       parse=FALSE, ...) {

     mapping <- NULL

     data <- NULL

     position <- "identity"

@@ -46,14 +48,14 @@ geom_strip <- function(taxa1, taxa2, label=NA, offset=0, offset.text=0,

                                     align=align, size=fontsize, barextend=barextend, angle=angle, family=family,

                                     mapping=mapping, data=data, geom=geom, hjust=hjust,

                                     position=position, show.legend = show.legend,

-                                    inherit.aes = inherit.aes, na.rm=na.rm, ...)

+                                    inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...)

     } else {

         layer_text <- stat_stripText(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset+offset.text,

                                     align=align, size=fontsize, barextend=barextend, angle=angle, fill=fill,family=family,

                                     mapping=mapping, data=data, geom=geom, hjust=hjust,

                                     position=position, show.legend = show.legend,

-                                    inherit.aes = inherit.aes, na.rm=na.rm, ...)

+                                    inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...)

     }

     list(

@@ -66,7 +68,7 @@ geom_strip <- function(taxa1, taxa2, label=NA, offset=0, offset.text=0,

 stat_stripText <- function(mapping=NULL, data=NULL,

                            geom="text", position="identity",

                            taxa1, taxa2, label, offset, align, barextend, ...,

-                           show.legend=NA, inherit.aes=FALSE, na.rm=FALSE) {

+                           show.legend=NA, inherit.aes=FALSE, na.rm=FALSE, parse=FALSE) {

     if (is.null(label) || is.na(label)) {

         default_aes <- aes_(x=~x, y=~y, node=~node, label=~label)

@@ -94,6 +96,7 @@ stat_stripText <- function(mapping=NULL, data=NULL,

                       align=align,

                       barextend=barextend,

                       na.rm=na.rm,