geom_cladelab: the devel version of geom_cladelabel to support aes mapping

[xiangpin]

geom_cladelab has support the original function of geom_cladelabel. But it also immits some new arguments to avoid confusion with argument of annot bar. They are barcolour or barcolor, controls the colour of bar; barsize, controls the size of barl; textcolour or textcolor, controls the colour of text; fontsize, controls the size of text; imagecolour or imagecolor control the colour of image, imagesize, controls the size of image. It also supports all the layouts.

library(ggtree)
library(ggplot2)
library(treeio)
library(patchwork)

set.seed(2015-12-21)
tree <- rtree(30)
data <- data.frame(id=c(45, 34),
                   annote=c("test clade", "another clade"),
                   image=c("7fb9bea8-e758-4986-afb2-95a2c3bf983d",
                           "0174801d-15a6-4668-bfe0-4c421fbe51e8"),
                   group=c("A", "B"),
                   offset=c(0.1, 0.1),
                   offset.text=c(0.1, 0.2))

p <- ggtree(tree) + xlim(NA, 7)

p1 <- p +
     geom_cladelab(node=45, label="test label") +
     geom_cladelab(node=34, label="another clade")

p2 <- p + geom_cladelab(data=data,
                        mapping=aes(
                             node=id,
                             label=annote,
                             color=group,
                             offset=offset,
                             offset.text=offset.text),
                        geom="shadowtext",
                        align=TRUE,
                        horizontal=FALSE,
                        angle=0
                       )
p3 <- p +
      geom_cladelabel(node=45, label="test label", align=T, angle=270, hjust='center', offset.text=.5, fontsize=8, barsize=1.5) +
      geom_cladelabel(node=34, label="another clade", align=T, angle=45)

p4 <- p + geom_cladelabel(node=34, label="another clade", align=T, geom='label', fill='lightblue')

p5 <- p1 / p3 / p4 / p2

[xiangpin]

It also provides text, label, shadowtext, image, phylopic as the potions of geom. And text also supports emoji parse.

[GuangchuangYu]

内部函数也可以写点文档，主要是给自己看的。用#' @nord标记一下，就不会生成man文件。

[xiangpin]

好的

[GuangchuangYu]

把geom_cladelabel换成geom_cladelab之后，颜色就出不来了。

[xiangpin]

得用textcolor跟barcolor才能同时上色，因为当时我想的是，有时候用户可能不想bar跟label一起上色，不同图层同时用一个color会混淆掉，所以我就加了textcolor,barcolor还有imagecolor。如果color没有在mapping里，用户想要设置颜色就需要用到这几个参数，如果用mapping了就可以用color来设置，这个会同时给bar跟label上色，如果此时只想保留label的颜色则可以用barcolor='black'来设置。

library(ggtree)
library(patchwork)
set.seed(123)
tr <- rtree(30)
                                                                                                                                                                                                        p1 <- ggtree(tr) + xlim(NA, 5.2) +
     geom_cladelab(node=41, label="chicken", parse="emoji",
                   fontsize=6, align=TRUE, textcolor="firebrick", barcolor="firebrick") +
     geom_cladelab(node=53, label="duck", parse="emoji",
                   fontsize=6, align=TRUE, textcolor="steelblue", barcolor="steelblue") +
     geom_cladelab(node=48, label="family", parse="emoji",
                   fontsize=6, align=TRUE, textcolor="darkkhaki", barcolor="darkkhaki")

df <- data.frame(node=c(41, 53, 48),
                 labels=c("chicken", "duck", "family"))

p2 <- ggtree(tr) + xlim(NA, 5.2) +
      geom_cladelab(data=df,
                    mapping=aes(node=node, label=labels, color=labels),
                    parse="emoji",
                    fontsize=6,
                    align="TRUE"
                    ) +
      scale_color_manual(values=c("firebrick", "steelblue", "darkkhaki"),
                         guide="none")

p3 <- ggtree(tr) + xlim(NA, 5.2) +
      geom_cladelab(data=df,
                    mapping=aes(node=node, label=labels, color=labels),
                    parse="emoji",
                    fontsize=6,
                    align="TRUE",
                    barcolor="black") +
      scale_color_manual(values=c("firebrick", "steelblue", "darkkhaki"),
                         guide="none")

p <- p1 / p2 / p3
p