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

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

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

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

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

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

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

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

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

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

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

     list(

         if (show_segment){

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

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

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

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

             do.call("geom_segment2", lineparams)

@@ -1,33 +1,43 @@

-##' add tip label layer

+##' add tip label layer for a tree

+##'

+##' 'geom_tiplab' not only supports using text or label geom to display tip labels, 

+##' but also supports image geom to label tip with image files or phylopics.

+##'     

+##' For adding tip labels to a tree with circular layout, 'geom_tiplab' will 

+##' automatically adjust the angle of the tip labels to the tree by 

+##' internally calling 'geom_tiplab2'.

 ##'

 ##'

 ##' @title geom_tiplab

 ##' @param mapping aes mapping

-##' @param hjust horizontal adjustment

+##' @param hjust horizontal adjustment, defaults to 0

 ##' @param offset tiplab offset, horizontal 

-##' adjustment to nudge tip labels, default is 0.

-##' @param align align tip lab or not, logical

-##' @param linetype linetype for adding line if align = TRUE

-##' @param linesize line size of line if align = TRUE

+##' adjustment to nudge tip labels, defaults to 0

+##' @param align if TRUE, align all tip labels to the longest tip by adding padding characters 

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

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

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

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

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

-##' @param as_ylab display tip labels as y-axis label, only works for rectangular and dendrogram layouts

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

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

 ##' @param ... additional parameter

 ##'

 ##' additional parameters can refer the following parameters. 

 ##'

 ##' The following parameters for geom="text".

 ##' \itemize{

-##'     \item \code{size} control the size of tip labels, default is 3.88.

-##'     \item \code{colour} control the colour of tip labels, default is "black".

-##'     \item \code{angle} control the angle of tip labels, 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 

+##'     \item \code{size} control the size of tip labels, defaults to 3.88.

+##'     \item \code{colour} control the colour of tip labels, defaults to "black".

+##'     \item \code{angle} control the angle of tip labels, defaults to 0.

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

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

+##'     \item \code{family} the family of text, defaults to 'sans'.

+##'     \item \code{fontface} the font face of text, defaults to 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 .

-##'     \item \code{nudge_x} horizontal adjustment to nudge labels, default is 0. 

-##'     \item \code{nudge_y}  vertical adjustment to nudge labels, default is 0.

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

+##'     \item \code{nudge_x} horizontal adjustment to nudge labels, defaults to 0. 

+##'     \item \code{nudge_y}  vertical adjustment to nudge labels, defaults to 0.

 ##'     \item \code{check.overlap} if TRUE, text that overlaps previous text in the same layer 

 ##'      will not be plotted.

 ##'     \item \code{parse} if TRUE, the labels will be parsed into expressions, if it is 'emoji', the labels

@@ -36,49 +46,49 @@

 ##'

 ##' The following parameters for geom="label".

 ##' \itemize{

-##'     \item \code{size} the size of tip labels, default is 3.88.

-##'     \item \code{colour} the colour of tip labels, default is "black".

-##'     \item \code{fill} the colour of rectangular box of labels, default is "white".

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

-##'     \item \code{alpha} the transparency of labels, 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

+##'     \item \code{size} the size of tip labels, defaults to 3.88.

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

+##'     \item \code{fill} the colour of rectangular box of labels, defaults to "white".

+##'     \item \code{vjust} numeric vector specifying vertical justification, defaults to 0.5.

+##'     \item \code{alpha} the transparency of labels, defaults to NA.

+##'     \item \code{family} the family of text, defaults to 'sans'.

+##'     \item \code{fontface} the font face of text, defaults to 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.

-##'     \item \code{nudge_x} horizontal adjustment to nudge labels, default is 0.

-##'     \item \code{nudge_y}  vertical adjustment, default is 0.

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

+##'     \item \code{nudge_x} horizontal adjustment to nudge labels, defaults to 0.

+##'     \item \code{nudge_y}  vertical adjustment, defaults to 0.

 ##'     \item \code{check.overlap} if TRUE, text that overlaps previous text in the same layer

 ##'      will not be plotted.

 ##'     \item \code{parse} if TRUE, the labels will be parsed into expressions, if it is 'emoji', the labels

 ##'      will be parsed into emojifont.

-##'     \item \code{label.padding} Amount of padding around label, default is 'unit(0.25, "lines")'.

-##'     \item \code{label.r} Radius of rounded corners, default is 'unit(0.15, "lines")'.

-##'     \item \code{label.size} Size of label border, in mm, default is 0.25.

+##'     \item \code{label.padding} Amount of padding around label, defaults to 'unit(0.25, "lines")'.

+##'     \item \code{label.r} Radius of rounded corners, defaults to 'unit(0.15, "lines")'.

+##'     \item \code{label.size} Size of label border, in mm, defaults to 0.25.

 ##' }

 ##'

 ##' The following parameters for geom="shadowtext", some parameters are like to geom="text".

 ##' \itemize{

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

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

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

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

 ##' }

 ##'

 ##' The following parameters for geom="image" or geom="phylopic".

 ##' \itemize{

 ##'     \item \code{image} the image file path for geom='image', but when geom='phylopic',

 ##'      it should be the uid of phylopic databases.

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

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

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

+##'     \item \code{size} the image size, defaults to 0.05.

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

+##'     \item \code{alpha} the transparency of image, defaults to 0.8.

 ##' }

 ##'

 ##' The following parameters for the line when align = TRUE.

 ##' \itemize{

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

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

+##'     \item \code{colour} the colour of line, defaults to 'black'.

+##'     \item \code{alpha} the transparency of line, defaults to NA.

 ##'     \item \code{arrow} specification for arrow heads, 

-##'     as created by arrow(), default is NULL.

+##'     as created by arrow(), defaults to NULL.

 ##'     \item \code{arrow.fill} fill color to usse for the arrow head (if closed), 

-##'     default is 'NULL', meaning use 'colour' aesthetic.

+##'     defaults to 'NULL', meaning use 'colour' aesthetic.

 ##' }

 ##' @return tip label layer

 ##' @importFrom ggplot2 geom_text

@@ -89,6 +99,10 @@

 ##' require(ape)

 ##' tr <- rtree(10)

 ##' ggtree(tr) + geom_tiplab()

+##' @references 

+##'  For more detailed demonstration, please refer to chapter 4.3.3 of 

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

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

 geom_tiplab <- function(mapping=NULL, hjust = 0,  align = FALSE, linetype = "dotted",

                         linesize=0.5, geom="text",  offset=0, as_ylab = FALSE, ...) {

     structure(list(mapping = mapping,

@@ -210,14 +224,21 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE,

 ##' add tip label for circular layout

 ##'

+##' 'geom_tiplab2' will automatically adjust the angle of the tip labels 

+##' to the tree with circular layout

 ##'

 ##' @title geom_tiplab2

 ##' @param mapping aes mapping

-##' @param hjust horizontal adjustment

+##' @param hjust horizontal adjustment, defaults to 0

 ##' @param ... additional parameter, see geom_tiplab

 ##' @return tip label layer

 ##' @export

 ##' @author Guangchuang Yu

+##' @examples 

+##' library(ggtree)

+##' set.seed(123)

+##' tr <- rtree(10)

+##' ggtree(tr, layout = "circular") + geom_tiplab2()

 ##' @references <https://groups.google.com/forum/#!topic/bioc-ggtree/o35PV3iHO-0>

 ##' @seealso [geom_tiplab]

 geom_tiplab2 <- function(mapping=NULL, hjust=0, ...) {

@@ -263,10 +284,10 @@ geom_tiplab_circular <- geom_tiplab2

 #' Padding taxa labels

 #'

-#' This function add padding character to the left side of taxa labels.

+#' This function adds padding characters to the left side of taxa labels, adjust their length to the longest label.

 #' @param label taxa label 

-#' @param justify should a character vector be left-justified, right-justified (default), centred or left alone.

-#' @param pad padding character (default is a dot)

+#' @param justify should a character vector be right-justified (default), left-justified, centred or left alone.

+#' @param pad padding character (defaults to dots)

 #'

 #' @return Taxa labels with padding characters added

 #' @export

@@ -178,8 +178,8 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE,

                                node = node,

                                label = label,

                                subset = isTip)

-        if (!is.null(mapping))

-            segment_mapping <- modifyList(segment_mapping, mapping)

+        if (!is.null(text_mapping))

+            segment_mapping <- modifyList(segment_mapping, text_mapping)

     }

     imageparams <- list(mapping=text_mapping, hjust = hjust, nudge_x = offset, stat = StatTreeData)

     imageparams <- extract_params(imageparams, params, c("data", "size", "alpha", "color", "colour", "image", 

@@ -194,7 +194,7 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE,

     list(

         if (show_segment){

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

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

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

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

             do.call("geom_segment2", lineparams)

         }

@@ -182,19 +182,19 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE,

             segment_mapping <- modifyList(segment_mapping, mapping)

     }

     imageparams <- list(mapping=text_mapping, hjust = hjust, nudge_x = offset, stat = StatTreeData)

-    imageparams <- extract_params(imageparams, params, c("size", "alpha", "color", "colour", "image", 

+    imageparams <- extract_params(imageparams, params, c("data", "size", "alpha", "color", "colour", "image", 

                                                          "angle", "position", "inherit.aes", "by", "show.legend",

                                                          "image_fun", ".fun", "asp", "nudge_y", "height", "na.rm")) 

     labelparams <- list(mapping=text_mapping, hjust = hjust, nudge_x = offset, stat = StatTreeData)

     labelparams <- extract_params(labelparams, params, 

-                                  c("size", "alpha", "vjust", "color", "colour", "angle", "alpha", "family", "fontface",

+                                  c("data", "size", "alpha", "vjust", "color", "colour", "angle", "alpha", "family", "fontface",

                                     "lineheight", "fill", "position", "nudge_y", "show.legend", "check_overlap",

                                     "parse", "inherit.aes", "na.rm", "label.r", "label.size", "label.padding",

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

     list(

         if (show_segment){

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

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

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

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

             do.call("geom_segment2", lineparams)

         }

@@ -114,7 +114,7 @@ geom_tiplab_as_ylab <- function(hjust = 0, position = "right", ...) {

 geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE, 

                                     linetype = "dotted", linesize=0.5, geom="text",  

-                                    offset=0, family = "", fontface = "plain", 

+                                    offset=0, #family = "", fontface = "plain", 

                                     node="external", ...) {

     params <- list(...)

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

@@ -185,9 +185,9 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE,

     imageparams <- extract_params(imageparams, params, c("size", "alpha", "color", "colour", "image", 

                                                          "angle", "position", "inherit.aes", "by", "show.legend",

                                                          "image_fun", ".fun", "asp", "nudge_y", "height", "na.rm")) 

-    labelparams <- list(mapping=text_mapping, hjust = hjust, nudge_x = offset, stat = StatTreeData, family = family, fontface = fontface)

+    labelparams <- list(mapping=text_mapping, hjust = hjust, nudge_x = offset, stat = StatTreeData)

     labelparams <- extract_params(labelparams, params, 

-                                  c("size", "alpha", "vjust", "color", "colour", "angle", "alpha", 

+                                  c("size", "alpha", "vjust", "color", "colour", "angle", "alpha", "family", "fontface",

                                     "lineheight", "fill", "position", "nudge_y", "show.legend", "check_overlap",

                                     "parse", "inherit.aes", "na.rm", "label.r", "label.size", "label.padding",

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

@@ -91,10 +91,6 @@

 ##' ggtree(tr) + geom_tiplab()

 geom_tiplab <- function(mapping=NULL, hjust = 0,  align = FALSE, linetype = "dotted",

                         linesize=0.5, geom="text",  offset=0, as_ylab = FALSE, ...) {

-    #####in order to check whether it is geom_nodelab

-    #.call <- match.call(call = sys.call(sys.parent(1)))

-    #nodelab <- ifelse(as.list(.call)[[1]]=="geom_nodelab", TRUE, FALSE)

-    #####

     structure(list(mapping = mapping,

                    hjust = hjust,

                    align = align,

@@ -103,7 +99,7 @@ geom_tiplab <- function(mapping=NULL, hjust = 0,  align = FALSE, linetype = "dot

                    geom = geom,

                    offset = offset,

                    as_ylab = as_ylab,

-                   #nodelab = nodelab,

+				   node = "external",

                    ...),

               class = "tiplab")

 }

@@ -118,7 +114,8 @@ geom_tiplab_as_ylab <- function(hjust = 0, position = "right", ...) {

 geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE, 

                                     linetype = "dotted", linesize=0.5, geom="text",  

-                                    offset=0, family = "", fontface = "plain", ...) {

+                                    offset=0, family = "", fontface = "plain", 

+                                    node="external", ...) {

     params <- list(...)

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

         if (offset != 0){

@@ -143,28 +140,26 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE,

         label_geom <- get_fun_from_pkg("ggimage", "geom_phylopic")

     }

-

+    nodelab <- node

     x <- y <- label <- isTip <- node <- NULL

     if (align == TRUE) {

         self_mapping <- aes(x = max(x, na.rm=TRUE) + diff(range(x, na.rm=TRUE))/200, y = y,

-                            label = label, node = node, subset = isTip)

+                            label = label, node = node)#, subset = isTip)

     }

     else {

         self_mapping <- aes(x = x + diff(range(x, na.rm=TRUE))/200, y= y,

-                            label = label, node = node, subset = isTip)

-    }

-    if ("nodelab" %in% names(params) && params[["nodelab"]]){

-        # for node label

-        subset <- aes_string(subset="!isTip")

-    }else{

-        # for tip label

-        subset <- aes_string(subset="isTip")

+                            label = label, node = node)#, subset = isTip)

     }

+    subset <- switch(nodelab,

+					 internal = aes_string(subset="!isTip"),

+					 external = aes_string(subset="isTip"),

+					 all = aes_string(subset=NULL)

+					 )

     self_mapping <- modifyList(self_mapping, subset)

     if (is.null(mapping)) {

         text_mapping <- self_mapping

     } else {

-        if (!is.null(mapping$subset)){

+        if (!is.null(mapping$subset) && nodelab != "all"){

             newsubset <- aes_string(subset=paste0(as.expression(get_aes_var(mapping, "subset")), 

                                                   '&', 

                                                   as.expression(get_aes_var(subset, "subset")))

@@ -186,7 +181,6 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE,

         if (!is.null(mapping))

             segment_mapping <- modifyList(segment_mapping, mapping)

     }

-    params[["nodelab"]] <- NULL

     imageparams <- list(mapping=text_mapping, hjust = hjust, nudge_x = offset, stat = StatTreeData)

     imageparams <- extract_params(imageparams, params, c("size", "alpha", "color", "colour", "image", 

                                                          "angle", "position", "inherit.aes", "by", "show.legend",

@@ -92,8 +92,8 @@

 geom_tiplab <- function(mapping=NULL, hjust = 0,  align = FALSE, linetype = "dotted",

                         linesize=0.5, geom="text",  offset=0, as_ylab = FALSE, ...) {

     #####in order to check whether it is geom_nodelab

-    .call <- match.call(call = sys.call(sys.parent(1)))

-    nodelab <- ifelse(as.list(.call)[[1]]=="geom_nodelab", TRUE, FALSE)

+    #.call <- match.call(call = sys.call(sys.parent(1)))

+    #nodelab <- ifelse(as.list(.call)[[1]]=="geom_nodelab", TRUE, FALSE)

     #####

     structure(list(mapping = mapping,

                    hjust = hjust,

@@ -103,7 +103,7 @@ geom_tiplab <- function(mapping=NULL, hjust = 0,  align = FALSE, linetype = "dot

                    geom = geom,

                    offset = offset,

                    as_ylab = as_ylab,

-                   nodelab = nodelab,

+                   #nodelab = nodelab,

                    ...),

               class = "tiplab")

 }

@@ -122,10 +122,10 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE,

     params <- list(...)

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

         if (offset != 0){

-            warning_wrap("The nudge_x and offset argument both was provided.

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

                          Because they all adjust the horizontal offset of labels,

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

-                         'nudge_x' will be predetermined, 'offset' will be deprecated.")

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

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

         }

         offset <- params$nudge_x

         params$nudge_x <- NULL

@@ -4,7 +4,8 @@

 ##' @title geom_tiplab

 ##' @param mapping aes mapping

 ##' @param hjust horizontal adjustment

-##' @param offset tiplab offset

+##' @param offset tiplab offset, horizontal 

+##' adjustment to nudge tip labels, default is 0.

 ##' @param align align tip lab or not, logical

 ##' @param linetype linetype for adding line if align = TRUE

 ##' @param linesize line size of line if align = TRUE

@@ -25,8 +26,8 @@

 ##'     \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 .

-##'     \item \code{nudge_x} horizontal adjustment, default is 0.

-##'     \item \code{nudge_y}  vertical adjustment, default is 0.

+##'     \item \code{nudge_x} horizontal adjustment to nudge labels, default is 0. 

+##'     \item \code{nudge_y}  vertical adjustment to nudge labels, default is 0.

 ##'     \item \code{check.overlap} if TRUE, text that overlaps previous text in the same layer 

 ##'      will not be plotted.

 ##'     \item \code{parse} if TRUE, the labels will be parsed into expressions, if it is 'emoji', the labels

@@ -44,7 +45,7 @@

 ##'     \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.

-##'     \item \code{nudge_x} horizontal adjustment, default is 0.

+##'     \item \code{nudge_x} horizontal adjustment to nudge labels, default is 0.

 ##'     \item \code{nudge_y}  vertical adjustment, default is 0.

 ##'     \item \code{check.overlap} if TRUE, text that overlaps previous text in the same layer

 ##'      will not be plotted.

@@ -119,6 +120,16 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE,

                                     linetype = "dotted", linesize=0.5, geom="text",  

                                     offset=0, family = "", fontface = "plain", ...) {

     params <- list(...)

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

+        if (offset != 0){

+            warning_wrap("The nudge_x and offset argument both was provided.

+                         Because they all adjust the horizontal offset of labels,

+                         and the 'nudge_x' is consistency with 'ggplot2'. The

+                         'nudge_x' will be predetermined, 'offset' will be deprecated.")

+        }

+        offset <- params$nudge_x

+        params$nudge_x <- NULL

+    }

     geom <- match.arg(geom, c("text", "label", "shadowtext", "image", "phylopic"))

     if (geom == "text") {

         label_geom <- geom_text2

@@ -178,12 +189,12 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE,

     params[["nodelab"]] <- NULL

     imageparams <- list(mapping=text_mapping, hjust = hjust, nudge_x = offset, stat = StatTreeData)

     imageparams <- extract_params(imageparams, params, c("size", "alpha", "color", "colour", "image", 

-                                                         "angle", "nudge_x", "inherit.aes", "by", "show.legend",

+                                                         "angle", "position", "inherit.aes", "by", "show.legend",

                                                          "image_fun", ".fun", "asp", "nudge_y", "height", "na.rm")) 

     labelparams <- list(mapping=text_mapping, hjust = hjust, nudge_x = offset, stat = StatTreeData, family = family, fontface = fontface)

     labelparams <- extract_params(labelparams, params, 

                                   c("size", "alpha", "vjust", "color", "colour", "angle", "alpha", 

-                                    "lineheight", "fill", "nudge_x", "nudge_y", "show.legend", "check_overlap",

+                                    "lineheight", "fill", "position", "nudge_y", "show.legend", "check_overlap",

                                     "parse", "inherit.aes", "na.rm", "label.r", "label.size", "label.padding",

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

     list(

@@ -11,6 +11,74 @@

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

 ##' @param as_ylab display tip labels as y-axis label, only works for rectangular and dendrogram layouts

 ##' @param ... additional parameter

+##'

+##' additional parameters can refer the following parameters. 

+##'

+##' The following parameters for geom="text".

+##' \itemize{

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

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

+##'     \item \code{angle} control the angle of tip labels, 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 .

+##'     \item \code{nudge_x} horizontal adjustment, default is 0.

+##'     \item \code{nudge_y}  vertical adjustment, default is 0.

+##'     \item \code{check.overlap} if TRUE, text that overlaps previous text in the same layer 

+##'      will not be plotted.

+##'     \item \code{parse} if TRUE, the labels will be parsed into expressions, if it is 'emoji', the labels

+##'      will be parsed into emojifont.

+##' }

+##'

+##' The following parameters for geom="label".

+##' \itemize{

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

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

+##'     \item \code{fill} the colour of rectangular box of labels, default is "white".

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

+##'     \item \code{alpha} the transparency of labels, 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.

+##'     \item \code{nudge_x} horizontal adjustment, default is 0.

+##'     \item \code{nudge_y}  vertical adjustment, default is 0.

+##'     \item \code{check.overlap} if TRUE, text that overlaps previous text in the same layer

+##'      will not be plotted.

+##'     \item \code{parse} if TRUE, the labels will be parsed into expressions, if it is 'emoji', the labels

+##'      will be parsed into emojifont.

+##'     \item \code{label.padding} Amount of padding around label, default is 'unit(0.25, "lines")'.

+##'     \item \code{label.r} Radius of rounded corners, default is 'unit(0.15, "lines")'.

+##'     \item \code{label.size} Size of label border, in mm, default is 0.25.

+##' }

+##'

+##' The following parameters for geom="shadowtext", some parameters are like to geom="text".

+##' \itemize{

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

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

+##' }

+##'

+##' The following parameters for geom="image" or geom="phylopic".

+##' \itemize{

+##'     \item \code{image} the image file path for geom='image', but when geom='phylopic',

+##'      it should be the uid of phylopic databases.

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

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

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

+##' }

+##'

+##' The following parameters for the line when align = TRUE.

+##' \itemize{

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

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

+##'     \item \code{arrow} specification for arrow heads, 

+##'     as created by arrow(), default is NULL.

+##'     \item \code{arrow.fill} fill color to usse for the arrow head (if closed), 

+##'     default is 'NULL', meaning use 'colour' aesthetic.

+##' }

 ##' @return tip label layer

 ##' @importFrom ggplot2 geom_text

 ##' @importFrom utils modifyList

@@ -50,6 +118,7 @@ geom_tiplab_as_ylab <- function(hjust = 0, position = "right", ...) {

 geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE, 

                                     linetype = "dotted", linesize=0.5, geom="text",  

                                     offset=0, family = "", fontface = "plain", ...) {

+    params <- list(...)

     geom <- match.arg(geom, c("text", "label", "shadowtext", "image", "phylopic"))

     if (geom == "text") {

         label_geom <- geom_text2

@@ -73,14 +142,27 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE,

         self_mapping <- aes(x = x + diff(range(x, na.rm=TRUE))/200, y= y,

                             label = label, node = node, subset = isTip)

     }

-

+    if ("nodelab" %in% names(params) && params[["nodelab"]]){

+        # for node label

+        subset <- aes_string(subset="!isTip")

+    }else{

+        # for tip label

+        subset <- aes_string(subset="isTip")

+    }

+    self_mapping <- modifyList(self_mapping, subset)

     if (is.null(mapping)) {

         text_mapping <- self_mapping

     } else {

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

+            newsubset <- aes_string(subset=paste0(as.expression(get_aes_var(mapping, "subset")), 

+                                                  '&', 

+                                                  as.expression(get_aes_var(subset, "subset")))

+                                    )

+            self_mapping <- modifyList(self_mapping, newsubset)

+            mapping$subset <- NULL

+        }

         text_mapping <- modifyList(self_mapping, mapping)

     }

-

-

     show_segment <- FALSE

     if (align && (!is.na(linetype) && !is.null(linetype))) {

         show_segment <- TRUE

@@ -93,20 +175,29 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE,

         if (!is.null(mapping))

             segment_mapping <- modifyList(segment_mapping, mapping)

     }

-

+    params[["nodelab"]] <- NULL

+    imageparams <- list(mapping=text_mapping, hjust = hjust, nudge_x = offset, stat = StatTreeData)

+    imageparams <- extract_params(imageparams, params, c("size", "alpha", "color", "colour", "image", 

+                                                         "angle", "nudge_x", "inherit.aes", "by", "show.legend",

+                                                         "image_fun", ".fun", "asp", "nudge_y", "height", "na.rm")) 

+    labelparams <- list(mapping=text_mapping, hjust = hjust, nudge_x = offset, stat = StatTreeData, family = family, fontface = fontface)

+    labelparams <- extract_params(labelparams, params, 

+                                  c("size", "alpha", "vjust", "color", "colour", "angle", "alpha", 

+                                    "lineheight", "fill", "nudge_x", "nudge_y", "show.legend", "check_overlap",

+                                    "parse", "inherit.aes", "na.rm", "label.r", "label.size", "label.padding",

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

     list(

-        if (show_segment)

-            geom_segment2(mapping = segment_mapping,

-                          linetype = linetype, nudge_x = offset,

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

+        if (show_segment){

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

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

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

+            do.call("geom_segment2", lineparams)

+        }

        ,

         if (geom %in% c("image", "phylopic")) {

-            label_geom(mapping=text_mapping,

-                       hjust = hjust, nudge_x = offset, stat = StatTreeData, ...)            

+            do.call("label_geom", imageparams)

         } else {

-            label_geom(mapping=text_mapping,

-                       hjust = hjust, nudge_x = offset, stat = StatTreeData, 

-                       family = family, fontface = fontface, ...)

+            do.call("label_geom", labelparams)

         }

     )

 }

@@ -126,15 +217,17 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE,

 ##' @seealso [geom_tiplab]

 geom_tiplab2 <- function(mapping=NULL, hjust=0, ...) {

     params <- list(...)

-    if ("nodelab" %in% names(params) && params[["nodelab"]]){

-        # for geom_nodelab

-        subset1 <- "(!isTip & (angle < 90 | angle > 270))"

-        subset2 <- "(!isTip & (angle >= 90 & angle <= 270))"

-    }else{

-        # for geom_tiplab

-        subset1 <- "(isTip & (angle < 90 | angle > 270))"

-        subset2 <- "(isTip & (angle >= 90 & angle <=270))"

-    }

+    #if ("nodelab" %in% names(params) && params[["nodelab"]]){

+    #    # for geom_nodelab

+    #    subset1 <- "(!isTip & (angle < 90 | angle > 270))"

+    #    subset2 <- "(!isTip & (angle >= 90 & angle <= 270))"

+    #}else{

+    #    # for geom_tiplab

+    #    subset1 <- "(isTip & (angle < 90 | angle > 270))"

+    #    subset2 <- "(isTip & (angle >= 90 & angle <=270))"

+    #}

+    subset1 <- "(angle < 90 | angle > 270)"

+    subset2 <- "(angle >= 90 & angle <=270)"

     m1 <- aes_string(subset=subset1, angle="angle", node = "node")

     m2 <- aes_string(subset=subset2, angle="angle+180", node = "node")

@@ -148,7 +241,7 @@ geom_tiplab2 <- function(mapping=NULL, hjust=0, ...) {

         m1 <- modifyList(mapping, m1)

         m2 <- modifyList(mapping, m2)

     }

-    params[["nodelab"]] <- NULL

+    #params[["nodelab"]] <- NULL

     params1 <- params2 <- params

     params1[["mapping"]] <- m1

     params1[["hjust"]] <- hjust

@@ -195,3 +288,13 @@ label_pad <- function(label, justify = "right", pad = "\u00B7") {

     paste0(y, label)

 }

+

+extract_params <- function(originparam, inputparam, defaultparam){

+    if (any(defaultparam %in% names(inputparam))){

+        args <- intersect(defaultparam, names(inputparam))

+        originparam <- c(originparam, inputparam[names(inputparam) %in% args])

+    }

+    

+    return (originparam)

+

+}

@@ -126,7 +126,7 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE,

 ##' @seealso [geom_tiplab]

 geom_tiplab2 <- function(mapping=NULL, hjust=0, ...) {

     params <- list(...)

-    if (params[["nodelab"]]){

+    if ("nodelab" %in% names(params) && params[["nodelab"]]){

         # for geom_nodelab

         subset1 <- "(!isTip & (angle < 90 | angle > 270))"

         subset2 <- "(!isTip & (angle >= 90 & angle <= 270))"

@@ -22,6 +22,10 @@

 ##' ggtree(tr) + geom_tiplab()

 geom_tiplab <- function(mapping=NULL, hjust = 0,  align = FALSE, linetype = "dotted",

                         linesize=0.5, geom="text",  offset=0, as_ylab = FALSE, ...) {

+    #####in order to check whether it is geom_nodelab

+    .call <- match.call(call = sys.call(sys.parent(1)))

+    nodelab <- ifelse(as.list(.call)[[1]]=="geom_nodelab", TRUE, FALSE)

+    #####

     structure(list(mapping = mapping,

                    hjust = hjust,

                    align = align,

@@ -30,6 +34,7 @@ geom_tiplab <- function(mapping=NULL, hjust = 0,  align = FALSE, linetype = "dot

                    geom = geom,

                    offset = offset,

                    as_ylab = as_ylab,

+                   nodelab = nodelab,

                    ...),

               class = "tiplab")

 }

@@ -121,11 +126,12 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE,

 ##' @seealso [geom_tiplab]

 geom_tiplab2 <- function(mapping=NULL, hjust=0, ...) {

     params <- list(...)

-    nodelab <- ifelse("nodelab" %in% names(params), TRUE, FALSE)

-    if (nodelab){

+    if (params[["nodelab"]]){

+        # for geom_nodelab

         subset1 <- "(!isTip & (angle < 90 | angle > 270))"

         subset2 <- "(!isTip & (angle >= 90 & angle <= 270))"

     }else{

+        # for geom_tiplab

         subset1 <- "(isTip & (angle < 90 | angle > 270))"

         subset2 <- "(isTip & (angle >= 90 & angle <=270))"

     }

@@ -134,13 +140,8 @@ geom_tiplab2 <- function(mapping=NULL, hjust=0, ...) {

     if (!is.null(mapping)) {

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

-            if (nodelab){

-                newsubset1 <- paste0(as.expression(get_aes_var(mapping, "subset")), '& (angle < 90 | angle > 270)')

-                newsubset2 <- paste0(as.expression(get_aes_var(mapping, "subset")), '& (angle >= 90 & angle <= 270)')

-            }else{

-                newsubset1 <- paste0(as.expression(get_aes_var(mapping, "subset")), '& (isTip & (angle < 90 | angle > 270))')

-                newsubset2 <- paste0(as.expression(get_aes_var(mapping, "subset")), '& (isTip & (angle >= 90 & angle <= 270))')

-            }

+            newsubset1 <- paste0(as.expression(get_aes_var(mapping, "subset")), '&', subset1)

+            newsubset2 <- paste0(as.expression(get_aes_var(mapping, "subset")), '&', subset2)

             m1 <- aes_string(angle = "angle", node = "node", subset = newsubset1)

             m2 <- aes_string(angle = "angle+180", node = "node", subset = newsubset2)

         }

@@ -120,23 +120,41 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE,

 ##' @references <https://groups.google.com/forum/#!topic/bioc-ggtree/o35PV3iHO-0>

 ##' @seealso [geom_tiplab]

 geom_tiplab2 <- function(mapping=NULL, hjust=0, ...) {

-    angle <- isTip <- node <- NULL

-    m1 <- aes(subset=(isTip & (angle < 90 | angle > 270)), angle=angle, node = node)

-    m2 <- aes(subset=(isTip & (angle >= 90 & angle <=270)), angle=angle+180, node = node)

+    params <- list(...)

+    nodelab <- ifelse("nodelab" %in% names(params), TRUE, FALSE)

+    if (nodelab){

+        subset1 <- "(!isTip & (angle < 90 | angle > 270))"

+        subset2 <- "(!isTip & (angle >= 90 & angle <= 270))"

+    }else{

+        subset1 <- "(isTip & (angle < 90 | angle > 270))"

+        subset2 <- "(isTip & (angle >= 90 & angle <=270))"

+    }

+    m1 <- aes_string(subset=subset1, angle="angle", node = "node")

+    m2 <- aes_string(subset=subset2, angle="angle+180", node = "node")

     if (!is.null(mapping)) {

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

-            m1 <- aes_string(angle = "angle", node = "node",

-                             subset = paste0(as.expression(get_aes_var(mapping, "subset")), '& (isTip & (angle < 90 | angle > 270))'))

-            m2 <- aes_string(angle = "angle+180", node = "node",

-                             subset = paste0(as.expression(get_aes_var(mapping, "subset")), '& (isTip & (angle >= 90 & angle <= 270))'))

+            if (nodelab){

+                newsubset1 <- paste0(as.expression(get_aes_var(mapping, "subset")), '& (angle < 90 | angle > 270)')

+                newsubset2 <- paste0(as.expression(get_aes_var(mapping, "subset")), '& (angle >= 90 & angle <= 270)')

+            }else{

+                newsubset1 <- paste0(as.expression(get_aes_var(mapping, "subset")), '& (isTip & (angle < 90 | angle > 270))')

+                newsubset2 <- paste0(as.expression(get_aes_var(mapping, "subset")), '& (isTip & (angle >= 90 & angle <= 270))')

+            }

+            m1 <- aes_string(angle = "angle", node = "node", subset = newsubset1)

+            m2 <- aes_string(angle = "angle+180", node = "node", subset = newsubset2)

         }

         m1 <- modifyList(mapping, m1)

         m2 <- modifyList(mapping, m2)

     }

-

-    list(geom_tiplab_rectangular(m1, hjust=hjust, ...),

-         geom_tiplab_rectangular(m2, hjust=1-hjust, ...)

+    params[["nodelab"]] <- NULL

+    params1 <- params2 <- params

+    params1[["mapping"]] <- m1

+    params1[["hjust"]] <- hjust

+    params2[["mapping"]] <- m2

+    params2[["hjust"]] <- 1-hjust

+    list(do.call("geom_tiplab_rectangular", params1),

+         do.call("geom_tiplab_rectangular", params2)

          )

 }

@@ -161,7 +161,7 @@ geom_tiplab_circular <- geom_tiplab2

 #' tree <- rtree(5)

 #' tree$tip.label[2] <- "long string for test"

 #' label_pad(tree$tip.label)

-label_pad <- function(label, justify = "right", pad = "·") {

+label_pad <- function(label, justify = "right", pad = "\u00B7") {

     x <- format(label, 

                 width = max(nchar(label)),

                 justify = justify)

@@ -42,7 +42,9 @@ geom_tiplab_as_ylab <- function(hjust = 0, position = "right", ...) {

               )

 }

-geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE, linetype = "dotted", linesize=0.5, geom="text",  offset=0, fontface = "plain", ...) {

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

+                                    linetype = "dotted", linesize=0.5, geom="text",  

+                                    offset=0, family = "", fontface = "plain", ...) {

     geom <- match.arg(geom, c("text", "label", "shadowtext", "image", "phylopic"))

     if (geom == "text") {

         label_geom <- geom_text2

@@ -98,7 +100,8 @@ geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE, lin

                        hjust = hjust, nudge_x = offset, stat = StatTreeData, ...)            

         } else {

             label_geom(mapping=text_mapping,

-                       hjust = hjust, nudge_x = offset, stat = StatTreeData, fontface = fontface, ...)

+                       hjust = hjust, nudge_x = offset, stat = StatTreeData, 

+                       family = family, fontface = fontface, ...)

         }

     )

 }

@@ -139,3 +142,37 @@ geom_tiplab2 <- function(mapping=NULL, hjust=0, ...) {

 geom_tiplab_circular <- geom_tiplab2

+

+

+#' Padding taxa labels

+#'

+#' This function add padding character to the left side of taxa labels.

+#' @param label taxa label 

+#' @param justify should a character vector be left-justified, right-justified (default), centred or left alone.

+#' @param pad padding character (default is a dot)

+#'

+#' @return Taxa labels with padding characters added

+#' @export

+#' @author Guangchuang Yu and Yonghe Xia

+#' @references <https://groups.google.com/g/bioc-ggtree/c/INJ0Nfkq3b0/m/lXefnfV5AQAJ>

+#' @examples

+#' library(ggtree)

+#' set.seed(2015-12-21)

+#' tree <- rtree(5)

+#' tree$tip.label[2] <- "long string for test"

+#' label_pad(tree$tip.label)

+label_pad <- function(label, justify = "right", pad = "·") {

+    x <- format(label, 

+                width = max(nchar(label)),

+                justify = justify)

+    len <- vapply(gregexpr("^\\s+", x),

+                  attr, "match.length",

+                  FUN.VALUE = numeric(1))

+    len[len<0] <- 0

+    

+    y <- vapply(len, 

+                function(i) paste0(rep(pad, each=i), collapse = ''),

+                FUN.VALUE = character(1))

+    paste0(y, label)

+}

+

@@ -8,7 +8,7 @@

 ##' @param align align tip lab or not, logical

 ##' @param linetype linetype for adding line if align = TRUE

 ##' @param linesize line size of line if align = TRUE

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

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

 ##' @param as_ylab display tip labels as y-axis label, only works for rectangular and dendrogram layouts

 ##' @param ... additional parameter

 ##' @return tip label layer

@@ -43,11 +43,13 @@ geom_tiplab_as_ylab <- function(hjust = 0, position = "right", ...) {

 }

 geom_tiplab_rectangular <- function(mapping=NULL, hjust = 0,  align = FALSE, linetype = "dotted", linesize=0.5, geom="text",  offset=0, fontface = "plain", ...) {

-    geom <- match.arg(geom, c("text", "label", "image", "phylopic"))

+    geom <- match.arg(geom, c("text", "label", "shadowtext", "image", "phylopic"))

     if (geom == "text") {

         label_geom <- geom_text2

     } else if (geom == "label") {

         label_geom <- geom_label2

+    } else if (geom == 'shadowtext') {

+        label_geom <- get_fun_from_pkg("shadowtext", "geom_shadowtext")

     } else if (geom == "image") {

         label_geom <- get_fun_from_pkg("ggimage", "geom_image")

     } else if (geom == "phylopic") {

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

 ##' @param linetype linetype for adding line if align = TRUE

 ##' @param linesize line size of line if align = TRUE

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

-##' @param as_ylab display tip labels as y-axis label, only works for rectangular layout

+##' @param as_ylab display tip labels as y-axis label, only works for rectangular and dendrogram layouts

 ##' @param ... additional parameter

 ##' @return tip label layer

 ##' @importFrom ggplot2 geom_text

@@ -9,6 +9,7 @@

 ##' @param linetype linetype for adding line if align = TRUE

 ##' @param linesize line size of line if align = TRUE

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

+##' @param as_ylab display tip labels as y-axis label, only works for rectangular layout