@@ -20,15 +20,12 @@ Imports:

     ape,

     dplyr,

     ggplot2 (>= 3.0.0),

-    grDevices,

     grid,

     magrittr,

     methods,

     purrr,

     rlang,

     rvcheck (>= 0.1.0),

-    scales,

-    tibble,

     tidyr,

     tidytree (>= 0.1.9),

     treeio (>= 1.3.14),

@@ -37,10 +34,13 @@ Suggests:

     emojifont,

     ggimage,

     ggplotify,

+    grDevices,

     knitr,

     prettydoc,

     rmarkdown,

-    testthat

+    scales,

+    testthat,

+    tibble

 Remotes:

     GuangchuangYu/treeio

 VignetteBuilder: knitr

@@ -190,7 +190,6 @@ importFrom(ggplot2,xlab)

 importFrom(ggplot2,xlim)

 importFrom(ggplot2,ylab)

 importFrom(ggplot2,ylim)

-importFrom(grDevices,colorRampPalette)

 importFrom(graphics,identify)

 importFrom(grid,convertX)

 importFrom(grid,convertY)

@@ -214,9 +213,6 @@ importFrom(methods,setGeneric)

 importFrom(methods,setOldClass)

 importFrom(rlang,.data)

 importFrom(rvcheck,get_aes_var)

-importFrom(rvcheck,get_fun_from_pkg)

-importFrom(scales,alpha)

-importFrom(tibble,data_frame)

 importFrom(tidyr,gather)

 importFrom(tidytree,MRCA)

 importFrom(tidytree,as_tibble)

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

 ##' @param ... additional parameters

 ##' @return geom layer

 ##' @export

-##' @author guangchuang yu

+##' @author Guangchuang Yu

 geom_motif <- function(mapping, data, on, ...) {

     if (is.null(unlist(mapping)$y)) {

         seqnames <- as.character(unlist(mapping)$group)

@@ -107,7 +107,7 @@ scale_x_ggtree <- function(tree_view, breaks=NULL, labels=NULL) {

     }

     if (is.null(breaks)) {

-        breaks <- hist(x, breaks=5, plot=FALSE)$breaks

+        breaks <- graphics::hist(x, breaks=5, plot=FALSE)$breaks

     }

     m <- attr(p, "mapping")

@@ -266,8 +266,7 @@ coplot <- function(tree1, tree2, hjust=0) {

 ##' @param alpha transparency of color

 ##' @return updated ggtree object

 ##' @export

-##' @importFrom scales alpha

-##' @author guangchuang yu

+##' @author Guangchuang Yu

 set_hilight_legend <- function(p, color, label, alpha=1) {

 	d <- data.frame(color=color, clade=label, x=0, y=1, alpha=alpha)

 	p + geom_rect(aes_(fill=~clade, xmin=~x, xmax=~x, ymin=~y, ymax=~y), data=d, inherit.aes=F) +

@@ -3,13 +3,12 @@

 ### draw_key_hack

-##' @importFrom scales alpha

 ##' @importFrom grid grobTree

 ##' @importFrom grid rectGrob

 ##' @importFrom grid gpar

 draw_key_hack <- function(data, params, size) {

   print('draw_key_hack') ##DEBUG

-  data$fill <- alpha(data$fill, data$alpha)

+  data$fill <- scales::alpha(data$fill, data$alpha)

   data$alpha <- 1

   grobTree(

@@ -1,7 +1,6 @@

 ##' @importFrom ape ladderize

 ##' @importFrom treeio as.phylo

 ##' @importFrom treeio Nnode

-##' @importFrom tibble data_frame

 ##' @importFrom dplyr full_join

 ##' @importFrom dplyr mutate_

 ##' @importFrom tidytree as_tibble

@@ -40,7 +39,7 @@ fortify.phylo <- function(model, data,

         ypos <- getYcoord(x)

         N <- Nnode(x, internal.only=FALSE)

-        xypos <- data_frame(node=1:N, x=xpos, y=ypos)

+        xypos <- tibble::data_frame(node=1:N, x=xpos, y=ypos)

         df <- as_tibble(model) %>%

             mutate_(isTip = ~(! node %in% parent))

@@ -117,7 +117,7 @@ msaplot <- function(p, fasta, offset=0, width=1, color=NULL, window=NULL, bg_lin

                        data=msa.df, inherit.aes = FALSE) +

                                scale_fill_manual(values=color)

-    breaks <- hist(seq_along(slice), breaks=10, plot=FALSE)$breaks

+    breaks <- graphics::hist(seq_along(slice), breaks=10, plot=FALSE)$breaks

     pos <- start + breaks * width

     mapping <- data.frame(from=breaks+1, to=pos)

     attr(p, "mapping") <- mapping

@@ -93,7 +93,7 @@ roundDigit <- function(d) {

 ## from ChIPseeker

-##' @importFrom grDevices colorRampPalette

+## @importFrom grDevices colorRampPalette

 getCols <- function (n) {

     col <- c("#8dd3c7", "#ffffb3", "#bebada", "#fb8072", "#80b1d3",

              "#fdb462", "#b3de69", "#fccde5", "#d9d9d9", "#bc80bd",

@@ -104,12 +104,9 @@ getCols <- function (n) {

     col3 <- c("#a6cee3", "#1f78b4", "#b2df8a", "#33a02c", "#fb9a99",

               "#e31a1c", "#fdbf6f", "#ff7f00", "#cab2d6", "#6a3d9a",

               "#ffff99", "#b15928")

-    colorRampPalette(col3)(n)

+    grDevices::colorRampPalette(col3)(n)

 }

-##' @importFrom rvcheck get_fun_from_pkg

-hist <- get_fun_from_pkg("graphics", "hist")

-

 ##

 ##

@@ -22,5 +22,5 @@ geom layer

 geom layer to draw aligned motif

 }

 \author{

-guangchuang yu

+Guangchuang Yu

 }

@@ -22,5 +22,5 @@ updated ggtree object

 set legend for multiple geom_hilight layers

 }

 \author{

-guangchuang yu

+Guangchuang Yu

 }