@@ -94,7 +94,6 @@ export(stat_balance)

 export(stat_hilight)

 export(subview)

 export(theme_inset)

-export(theme_transparent)

 export(theme_tree)

 export(theme_tree2)

 export(viewClade)

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

 CHANGES IN VERSION 1.11.2

 ------------------------

- o deprecate subview, annotation_image and phylopic <2017-12-04, Mon>

+ o deprecate subview, annotation_image and phylopic; remove theme_transparent <2017-12-04, Mon>

  o geom_tiplab now supports geom = "image" or geom = "phylopic" <2017-12-04, Mon>

  o A new layer geom_nodelab that equivalent to geom_tiplab but works for internal node <2017-12-04, Mon>

@@ -47,16 +47,12 @@ plot_fantree <- function(fantree, upper=TRUE) {

         annotation_custom(ggplotGrob(fantree),

                           xmin=-.15, xmax=1.15,

                           ymin=ymin, ymax=ymax)

-    ## d <- data.frame(x=c(0,1), y=c(0.5, 1))

-    ## ggplot(d, aes_(x=~x, y=~y)) %>%

-    ##     subview(fantree, 0.5, y, width=2, height=2.2) ##  %>%

-    ## subview(p2+theme_transparent(), 0.5, 0.45, width=2, height=2.2) + theme_tree()

 }

 plot_fantrees <- function(uppertree, lowertree) {

     ggplot() + xlim(0,1) + ylim(0.5, 1) + theme_tree() +

         annotation_custom(ggplotGrob(uppertree), xmin=-.15, xmax=1.15, ymin=0.52, ymax=1.02) +

-        annotation_custom(ggplotGrob(lowertree + theme_transparent()), xmin=-.15, xmax=1.15, ymin=0.48, ymax=0.98)

+        annotation_custom(ggplotGrob(lowertree + ggimage::theme_transparent()), xmin=-.15, xmax=1.15, ymin=0.48, ymax=0.98)

 }

@@ -77,32 +77,6 @@ theme_tree2_internal <- function(bgcolor="white", fgcolor="black",

               ...)

 }

-##' transparent background theme

-##'

-##'

-##' @title theme_transparent

-##' @param ... additional parameter to tweak the theme

-##' @return ggplot object

-##' @importFrom ggplot2 theme

-##' @importFrom ggplot2 element_rect

-##' @export

-##' @author Guangchuang Yu

-theme_transparent <- function(...) {

-    message("this theme was moved to ggimage::theme_transparent and will be removed in next release")

-

-    theme(panel.background = element_rect(

-              fill = "transparent",

-              colour = NA),

-          plot.background = element_rect(

-              fill = "transparent",

-              colour = NA),

-          legend.key = element_rect(

-              fill = "transparent",

-              colour = NA),

-          legend.background = element_rect(

-              fill = "transparent",

-              colour = NA), ...)

-}

 ##' inset theme

 ##'

@@ -113,10 +87,9 @@ theme_transparent <- function(...) {

 ##' @export

 ##' @author Guangchuang Yu

 theme_inset <- function(...) {

-    message("this theme will be removed in next release")

     list(xlab(NULL),

          ylab(NULL),

          theme_tree(...),

-         theme_transparent()

+         ggimage::theme_transparent()

          )

 }

deleted file mode 100644

@@ -1,20 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/theme.R

-\name{theme_transparent}

-\alias{theme_transparent}

-\title{theme_transparent}

-\usage{

-theme_transparent(...)

-}

-\arguments{

-\item{...}{additional parameter to tweak the theme}

-}

-\value{

-ggplot object

-}

-\description{

-transparent background theme

-}

-\author{

-Guangchuang Yu

-}