some questions about unrooted tree

[苏秦之]

Hi, I have some questions about unrooted tree. My code is as follows.

treeg <- read.tree("genome_fasttree.txt")

groupg <- read.table("genome_tree_annotation.txt",header=T,sep="\t")

groupginfo_g <-split(groupg$strain,groupg$species)

treegg<-ggtree(treeg,layout="daylight",size=3,branch.length='none')

treegg_group<-groupOTU(treegg,groupginfo_g,'host')+aes(color=host)+

  scale_color_manual(values=c("#1a1a1a","#f46d43","#3288bd","#1a9850","#c51b7d"))+

  geom_tiplab(size=8)+

  theme(legend.position="right")

pg<-treegg_group+new_scale_fill()

pg1<-pg+new_scale_color()

cluster<-groupg[,c(2,3)]

pg2<-pg1 %<+% cluster +

  geom_tippoint(aes(color=cluster,shape=cluster),alpha=.7,shape=16)+

  scale_color_manual(breaks=c("Gillia_Acer_1","Gillia_Acer_2","Gillia_Acer_3","Gillia_Acer_4","Gillia_Acer_5","none"),values=c("#66c2a5","#8da0cb","#e78ac3","#a6d854","#ffd92f","#737373"))+

  scale_shape_manual(breaks=c("Gillia_Acer_1","Gillia_Acer_2","Gillia_Acer_3","Gillia_Acer_4","Gillia_Acer_5","NA"),values=c(21,22,23,24,25,21))

pg2

ggsave("genome_tree2.pdf",treegg_group,width=48,height=40)

I have two problems. 

First, my tip label embedded in the branches as the picture.

Second, the error information as follows:

> pg2
错误: Insufficient values in manual scale. 11 needed but only 6 provided.

I don't know how to solve the problems. Thank you for your help.

[Yu, Guangchuang]

reproducible example pls.

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1. G Yu*, TTY Lam, H Zhu, Y Guan*. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution, 2018, 35(2):3041-3043. doi: 10.1093/molbev/msy194
2. G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data, Methods in Ecology and Evolution, 2017, 8(1):28-36. doi:10.1111/2041-210X.12628
3. Book: https://yulab-smu.github.io/treedata-book/
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Guangchuang Yu PhD

Professor
School of Basic Medical Sciences

Southern Medical University

Guangzhou, China

www: https://guangchuangyu.github.io

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