使用 ggtree 时，“错误：必须从色调调色板中请求至少一种颜色”

如何解决使用 ggtree 时，“错误：必须从色调调色板中请求至少一种颜色”

我正在尝试创建一个系统发育树，为不同的背部模式显示不同颜色的尖端点，当我几周前第一次尝试时，它工作得很好，但现在尝试它我得到了上面的错误代码。自上次以来，我唯一做的不同是更新了一些软件包。

我使用的代码如下：

ggtree(frogtree.2,layout="circular") %<+% frogdata + geom_tiplab(offset = .3,hjust = .6) + theme(legend.position = "right") + geom_tippoint(aes(colour=PATTERN))

基于此错误的其他查询，我的数据中没有 NA，树加载良好，直到我使用 geom_tippoint(aes(fill = PATTERN))

由于此代码以前有效并且我没有更改数据的结构（字符和数字），我不确定问题出在哪里。

数据片段：

物种	微生境	颜色	模式
D.裂隙	WL	绿色	斑驳
E。指尖角	摇滚	绿色	制服
E。安特列斯	摇滚	绿色	制服
E。阿特金西	WL	棕色	对称
E。坎皮	地球	白色	制服
E。烹饪	摇滚	棕色	制服

提前致谢。

编辑： 使用 dput 我来自“frogdata”的数据片段是：

>dput(frogdata[1:10,1:4 ])
structure(list(SPECIES = c("D. diastema","E. angustidigitorum","E. antillensis","E. atkinsi","E. campi","E. cooki","E. coqui","E. cystignathoides","E. flavescens","E. grandis"),FAMILY = c("Eleutherodactylidae ","Eleutherodactylidae","Eleutherodactylidae"
),MICROHABITAT = c("WL","rock","WL","earth","WL"),COLOUR = c("green","green","brown","white","brown"
)),row.names = c(NA,10L),class = "data.frame")

来自“frogtree.2”的片段是：

 dput(frogtree.2)
structure(list(edge = structure(c(97L,97L,96L,95L,94L,93L,92L,91L,90L,89L,88L,87L,86L,85L,84L,83L,82L,81L,80L,79L,78L,77L,76L,75L,74L,73L,72L,71L,70L,69L,68L,67L,66L,65L,64L,63L,62L,61L,60L,59L,58L,57L,56L,55L,54L,53L,52L,51L,50L,48L,49L,47L,45L,46L,44L,41L,42L,43L,38L,39L,37L,34L,35L,36L,40L,32L,33L,31L,28L,29L,27L,24L,25L,23L,22L,21L,19L,20L,16L,17L,15L,13L,14L,12L,10L,11L,9L,7L,8L,5L,6L,3L,4L,18L,26L,30L,1L,2L,52L),.Dim = c(96L,2L)),edge.length = c(0.03940155,0.03940155,0.04827143,0.00886988,0.048902435,0.0147448041666667,0.0153758091666667,0.066352673,0.00270543383333331,0.02971821,0.00824750499999999,0.037965715,0.0608982058333334,0.0325112478333334,0.026269995,0.0532619825,0.0269919875,0.088415535,0.0125160194117647,0.100931554411765,0.0476695719117647,0.0364101436041083,0.0384777771825397,0.129893066666667,0.06590009,0.071875705,0.00597561499999999,0.037936535,0.0796354725,0.0416989375,0.0927819333333333,0.0131464608333333,0.1262746025,0.0334926691666667,0.054465585,0.03967896,0.058724815,0.019045855,0.0171324,0.05103453,0.03390213,0.03775446,0.0327989822727273,0.0195189122727273,0.0705534422727273,0.027401475,0.025252155,0.015455835,0.029841255,0.020044935,0.00717716249999999,0.0250727775,0.0369889491666667,0.0189097593939394,0.0464202691666667,0.0771586558333334,0.0416082706560284,0.177491741489362,0.123026156489362,0.0396052220062134,0.0908223609955752,0.217096963495575,0.0137432219084653,0.15896448040404,0.23084018540404,0.0170589140269943,0.118006032764368,0.110557401415162,0.27845723,0.239645341276596,0.270203471845561),Nnode = 48L,node.label = c("Root","1.0000","","0.1400","0.0980","0.2500","0.9920","0.5120","0.2720","0.3240","0.7240","0.9960","0.9840","0.7300","0.5600","0.9700","0.6420","0.7140","0.9080","0.7860","0.9980","0.9800","0.9540","0.8500","0.6300","0.8520","0.9020","0.9720","0.5000","0.1660","0.2740","0.3160","0.1840","0.0940","0.2180","0.4860","0.3740","0.9520","0.6320","0.7100","0.4920","0.5640","0.6080","0.5080","0.8960"),tip.label = c("Pl._thaul","En._petersi","E._angustidigitorum","E._grandis","E._modestus","E._pallidus","E._nitidus","E._pipilans","E._longipes","E._campi","E._cystignathoides","E._marnockii","E._guttilatus","E._verrucipes","E._atkinsi","E._planirostris","E._rogersi","E._inoptatus","E._johnstonei","E._martinicensis","E._flavescens","E._antillensis","E._cooki","E._coqui","E._portoricensis","D._diastema","Pl._bufoninum","Pl._cinereum","Pl._brachyops","Le._fragilis","En._pustulosus","Ph._cuvieri","Ps._falcipes","Ad._andreae","Li._lineatus","Le._wagneri","Le._melanonotus","Le._latrans","Le._macrosternum","Le._insularum","Le._pentadactylus","Le._savagei","Le._knudseni","Le._latinasus","Le._albilabris","Le._mystacinus","Le._fuscus","Le._gracilis","Le._mystaceus")),class = "phylo",order = "postorder",RSS = 12.8678101120044)

这棵树是通过

作为newick文件导入的

read.tree("frog.tree.nwk")

我尝试使用的软件包是：

library(tidyverse)
library(ape)
library(caper)
library(geiger)
library(maps)
library(phytools)
library(picante)
library(stringr)
library(adegenet)
library(stats)
library(ips)
library(phylobase)
library(ade4)
library(caper)
library(geiger)
library(phytools)
library(vegan)
library(lattice)
library(nlme)
library(MASS)
library(scales)
library(treeplyr)
library(phangorn)

更新： 所以我使用@Skaqqs 提供的代码：

```dat.1 <- data.frame(SPECIES = frogtree.2$tip.label,PATTERN = sample(frogdata$PATTERN,size = length(frogtree.2$tip.label),replace = T))```

这适用于 ggtree 代码：

```ggtree(frogtree.2,layout="circular",branch.length = "none") %<+% dat.1 + geom_tiplab(offset = 7,hjust = .6) + geom_tippoint(aes(colour = PATTERN),cex = 4) + theme(legend.position = "right")```

但是 dat.1 DF 与我的数据集不一致，因此它生成的树无效。 我还想看看是否可以使用我的数据集（整个 DF 的完整 dput 输出）将 REGION 作为形状美学添加到树中：

```structure(list(SPECIES = structure(c(2L,.Label = c("Ad. Andreae","D.diastema","E. grandis","E. guttilatus","E. inoptatus","E. johnstonei","E. leprus","E. longipes","E. marnockii","E. martinicensis","E. modestus","E. nitidus","E. pallidus","E. pipilans","E. planirostris","E. portoricensis","E. rogersi","E. verrucipes","E.angustidigitorum","En. petersi","En. pustulosus","Le. albilabris","Le. fragilis","Le. fuscus","Le. iatrans","Le. insularum","Le. knudseni","Le. latinasus","Le. macrosternum","Le. melanonotus","Le. mystaceus ","Le. mystacinus","Le. pentadactylus","Le. savagei","Le. wagneri","Le.gracilis","Li. lineatus","Ph. cuvieri","Pl. brachyops","Pl. bufoninum","Pl. cinereum","Pl. thaul","Ps. falcipes"),class = "factor"),"Eleutherodactylidae"),MICROHABITAT = structure(c(7L,7L),.Label = c("earth","grass","LL","stones","surface",COLOUR = structure(c(3L,2L),.Label = c("beige","grey","orange","white"),PATTERN = structure(c(3L,3L),.Label = c("Barred","Complex","Mottled","Symmetrical","Uniform"),COLOUR.1 = structure(c(7L,9L),"black","peach","red","rufous","yellow"),TONE = c(55.5,56.3,30.5,31.9,38.6,33.9,58.3,45,55.7,58.7),disTANCE = c(1187.23,2185.09,2024.26,2285.65,3172.5,2039.48,2216.22,2264.15,2113.5,2147.5),REGION = structure(c(2L,.Label = c("Caribbean","Central America","north America","northern South America","Southern South America"),class = "factor")),class = "data.frame")```

然后我从我的数据集中创建了另一个 DF：

```dat <- data.frame(SPECIES = frogdata$SPECIES,PATTERN = frogdata$PATTERN,REGION=frogdata$REGION)```

绘制它：

```ggtree(frogtree.2,branch.length = "none") %<+% dat + geom_tiplab(offset = 7,hjust = .6) + geom_tippoint(aes(colour = PATTERN,shape=REGION),cex = 4) + theme(legend.position = "right")```

但我收到此警告消息： 警告信息：

```Removed 6 rows containing missing values (geom_point_g_gtree).```

还有这个数字：

https://i.stack.imgur.com/JxdCq.png

我看不出我的数据集有什么问题来获取此警告代码和缺少的提示点，我看不到任何 NA。

解决方法

我想我知道发生了什么。如果这不能解决您这边的问题，请告诉我，我们可以解决更多问题。您确定您使用的是完整版的 frogdata 吗？如果 frogdata 中的物种少于 frogtree.2，我会收到错误消息：

library(ggtree)

# frogtree.2 <- data.frame(...)

frogdata <- data.frame(
  SPECIES = c("D. diastema","E. angustidigitorum","E. antillensis","E. atkinsi","E. campi","E. cooki","E. coqui","E. cystignathoides","E. flavescens","E. grandis"),FAMILY = c("Eleutherodactylidae ","Eleutherodactylidae","Eleutherodactylidae"),MICROHABITAT = c("WL","rock","WL","earth","WL"),COLOUR = c("green","green","brown","white","brown"))

# Add pattern field
frogdata$PATTERN <- c("Mottled","Uniform","Symmetrical","Blank","Blank")

# Plot fails
ggtree(frogtree.2,layout="circular") %<+%
  frogdata +
  geom_tiplab(offset = .3,hjust = .6) +
  geom_tippoint(aes(colour = PATTERN)) +
  theme(legend.position = "right")
#> Error: Must request at least one colour from a hue palette.

但是当我使用树中的所有物种创建示例数据集时：

# Create new frogdata with same number of species as frogtree.2
dat <- data.frame(
  SPECIES = frogtree.2$tip.label,PATTERN = sample(frogdata$PATTERN,size = length(frogtree.2$tip.label),replace = TRUE))

# New plot
ggtree(frogtree.2,layout="circular") %<+%
  dat +
  geom_tiplab(offset = .3,hjust = .6) +
  geom_tippoint(aes(colour = PATTERN)) +
  theme(legend.position = "right")