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I am attempting to create a phylogeny tree that shows different coloured tip points for different dorsal patterns, when I first attempted this a few weeks ago it worked perfectly but trying it now I get the above error code. The only thing I have done differently since last time is updating some packages.

The code I am using is as follows:

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

Based from other queries on this error, I have no NAs in my data, the tree loads fine until I use geom_tippoint(aes(fill = PATTERN))

As this code has worked previously and I haven't changed the structure of the data (which is character and numerical) I am not sure where the problem lies.

Data snippet:

SPECIES MICROHABITAT COLOUR PATTERN
D. diastema WL Green Mottled
E. angustidigitorum Rock Green Uniform
E. antillensis Rock Green Uniform
E. atkinsi WL Brown Symmetrical
E. Campi Earth White Uniform
E. cooki Rock Brown Uniform

Thanks in advance.

Edit: From using dput my data snippet from 'frogdata' is:

>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", "Eleutherodactylidae", 
"Eleutherodactylidae", "Eleutherodactylidae", "Eleutherodactylidae", 
"Eleutherodactylidae", "Eleutherodactylidae", "Eleutherodactylidae"
), MICROHABITAT = c("WL", "rock", "rock", "WL", "earth", "earth", 
"rock", "WL", "WL", "WL"), COLOUR = c("green", "green", "green", 
"brown", "white", "brown", "brown", "green", "green", "brown"
)), row.names = c(NA, 10L), class = "data.frame")

snippet from 'frogtree.2' is:

 dput(frogtree.2)
structure(list(edge = structure(c(97L, 97L, 96L, 96L, 95L, 95L, 
94L, 94L, 93L, 93L, 92L, 92L, 91L, 91L, 90L, 90L, 89L, 89L, 88L, 
88L, 87L, 87L, 86L, 86L, 85L, 85L, 84L, 84L, 83L, 83L, 82L, 82L, 
81L, 81L, 80L, 80L, 79L, 79L, 78L, 78L, 77L, 77L, 76L, 76L, 75L, 
75L, 74L, 74L, 73L, 73L, 72L, 72L, 71L, 71L, 70L, 70L, 69L, 69L, 
68L, 68L, 67L, 67L, 66L, 66L, 65L, 65L, 64L, 64L, 63L, 63L, 62L, 
62L, 61L, 61L, 60L, 60L, 59L, 59L, 58L, 58L, 57L, 57L, 56L, 56L, 
55L, 55L, 54L, 54L, 53L, 53L, 52L, 52L, 51L, 51L, 50L, 50L, 48L, 
49L, 47L, 97L, 45L, 46L, 95L, 96L, 44L, 94L, 41L, 42L, 92L, 43L, 
91L, 93L, 38L, 39L, 37L, 89L, 34L, 35L, 87L, 36L, 86L, 88L, 85L, 
40L, 84L, 90L, 32L, 33L, 31L, 82L, 28L, 29L, 27L, 80L, 24L, 25L, 
23L, 78L, 22L, 77L, 21L, 76L, 19L, 20L, 16L, 17L, 15L, 73L, 13L, 
14L, 12L, 71L, 10L, 11L, 69L, 70L, 9L, 68L, 7L, 8L, 5L, 6L, 3L, 
4L, 64L, 65L, 63L, 66L, 62L, 67L, 61L, 72L, 60L, 18L, 59L, 74L, 
58L, 75L, 57L, 26L, 56L, 79L, 55L, 30L, 54L, 81L, 53L, 83L, 1L, 
2L, 51L, 52L), .Dim = c(96L, 2L)), edge.length = c(0.03940155, 
0.03940155, 0.04827143, 0.00886988, 0.048902435, 0.048902435, 
0.0147448041666667, 0.0153758091666667, 0.066352673, 0.00270543383333331, 
0.02971821, 0.02971821, 0.00824750499999999, 0.037965715, 0.0608982058333334, 
0.0325112478333334, 0.026269995, 0.026269995, 0.0532619825, 0.0269919875, 
0.088415535, 0.088415535, 0.0125160194117647, 0.100931554411765, 
0, 0.0476695719117647, 0, 0.100931554411765, 0.0364101436041083, 
0.0384777771825397, 0.129893066666667, 0.129893066666667, 0.129893066666667, 
0, 0.06590009, 0.06590009, 0.071875705, 0.00597561499999999, 
0.037936535, 0.037936535, 0.0796354725, 0.0416989375, 0.0927819333333333, 
0.0131464608333333, 0.1262746025, 0.0334926691666667, 0.054465585, 
0.054465585, 0.03967896, 0.03967896, 0.058724815, 0.019045855, 
0.0171324, 0.0171324, 0.05103453, 0.03390213, 0.03775446, 0.03775446, 
0.0327989822727273, 0.0195189122727273, 0.0705534422727273, 0, 
0.027401475, 0.027401475, 0.025252155, 0.025252155, 0.015455835, 
0.015455835, 0.029841255, 0.020044935, 0.00717716249999999, 0.0250727775, 
0.0369889491666667, 0.0189097593939394, 0.0464202691666667, 0.0771586558333334, 
0.0416082706560284, 0.177491741489362, 0, 0.123026156489362, 
0.0396052220062134, 0.0908223609955752, 0, 0.217096963495575, 
0.0137432219084653, 0.15896448040404, 0, 0.23084018540404, 0.0170589140269943, 
0.118006032764368, 0, 0.110557401415162, 0.27845723, 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", 
"1.0000", "0.9700", "0.6420", "0.7140", "0.9080", "0.7860", "0.9980", 
"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", "1.0000", "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)

This tree was imported as a newick file via

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

the packages I have tried using are:

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)

UPDATE: So I am using the code that @Skaqqs provided:

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

This works with the ggtree code:

```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")```

But the dat.1 DF does not align with my data set and so the tree it produces is not valid. I also wanted to see if i could add REGION as a shape aesthetic to the tree using my data set (full dput output for entire DF):

```structure(list(SPECIES = structure(c(2L, 26L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L), .Label = c("Ad. Andreae", "D.diastema", "E. antillensis", "E. atkinsi", "E. campi", "E. cooki", "E. coqui", "E. cystignathoides","E. flavescens", "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"), FAMILY = c("Eleutherodactylidae ", "Eleutherodactylidae", "Eleutherodactylidae", "Eleutherodactylidae", "Eleutherodactylidae", "Eleutherodactylidae", "Eleutherodactylidae", "Eleutherodactylidae", "Eleutherodactylidae", "Eleutherodactylidae"), MICROHABITAT = structure(c(7L, 4L, 4L, 7L, 1L, 1L, 4L, 7L, 7L, 7L), .Label = c("earth", "grass", "LL", "rock", "stones", "surface", "WL"), class = "factor"), COLOUR = structure(c(3L, 3L, 3L, 2L, 6L, 2L, 2L, 3L, 3L, 2L), .Label = c("beige", "brown", "green", "grey", "orange", "white"), class = "factor"), PATTERN = structure(c(3L, 5L, 5L, 4L, 5L, 5L, 4L, 3L, 2L, 3L), .Label = c("Barred", "Complex", "Mottled", "Symmetrical", "Uniform"), class = "factor"), COLOUR.1 = structure(c(7L, 3L, 6L, 3L, 4L, 3L, 1L, 1L, 10L, 9L), .Label = c("beige", "black", "brown", "green", "grey", "orange", "peach", "red", "rufous", "yellow"), class = "factor"), 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, 3L, 1L, 1L, 3L, 1L, 3L, 3L, 1L, 3L), .Label = c("Caribbean", "Central America", "North America", "Northern South America", "Southern South America"), class = "factor")), row.names = c(NA, 10L), class = "data.frame")```

I then created another DF from my data set:

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

Plotted it with:

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

But I get this warning message: Warning message:

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

And this figure:

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

I can't see what would be wrong with my data set to get this warning code and the missing tip points, there are no NAs that I can see.

Shannon Rae
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  • Are you able to share a MRE? https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example – Skaqqs Jul 06 '21 at 15:28
  • What other information would you need that isn't provided in the question? Apologies I have not been using R for very long. – Shannon Rae Jul 14 '21 at 13:41
  • An MRE contains all the code and data I would need to reproduce the issue you are facing. I see you provided a sample dataset, thank you! However, sharing data in an R-friendly way (such as using `dput()`; see examples in above link) will typically elicit more answers. One good way of thinking about this is to open a new script and enter all the information you provided in your question; is this enough to see the problem? Is the data snippet you shared an example of `frogtree.2`? What packages are needed? I'm looking forward to trying to help answer your question. Thanks! – Skaqqs Jul 14 '21 at 17:23
  • Hi, thank you so much for trying to help!! I have added my data and tree snippets in code form, I hope this is what you require! I also added the packages that I have loaded in previous attempts, I guess the prominant ones are tidyverse, ggtree, ggplot2 – Shannon Rae Jul 15 '21 at 13:44
  • Can you share the result of `dput(frogtree.2)` please? I can't make a tree with `frogdata`. – Skaqqs Jul 15 '21 at 16:30
  • Okay, done! You should find the output on the edited question. – Shannon Rae Jul 16 '21 at 09:49

1 Answers1

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I think I figured out what is going on. If this doesn't fix the problem on your side, let me know and we can troubleshoot more. Are you sure you are using the full version of frogdata? If there are fewer species in frogdata than frogtree.2, I get an error:

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", "Eleutherodactylidae", "Eleutherodactylidae", "Eleutherodactylidae", "Eleutherodactylidae", "Eleutherodactylidae", "Eleutherodactylidae", "Eleutherodactylidae"),
  MICROHABITAT = c("WL", "rock", "rock", "WL", "earth", "earth", "rock", "WL", "WL", "WL"),
  COLOUR = c("green", "green", "green", "brown", "white", "brown", "brown", "green", "green", "brown"))

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

But when I created an example dataset using all the species in your tree:

# 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")

frogdata 2

Skaqqs
  • 4,010
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  • Hey, sorry for the delay in response. I discovered that a species was missing from the tree, which I rectified. But, this code half worked, so it produced a tree similar to the one shown here but the species didn't match up to the correct body pattern. Is there a way to ensure the species are listed with their correct body pattern, using the original data set perhaps? I am facing another issue when attempting to use the original data set and rectified tree, I get a warning message: `Removed 6 rows containing missing values (geom_point_g_gtree)` I didn't get this error when using the above code – Shannon Rae Aug 03 '21 at 17:05
  • It would be great if you could update your original question with your current working code and any of the issues that you are seeing! After that I would be happy to try to figure out what's going on. – Skaqqs Aug 03 '21 at 17:43
  • Hey Skaqqs, I've updated the question! I hope it is clear. – Shannon Rae Aug 06 '21 at 12:02
  • I see your updates in the question, thanks! How is `frogtree.2` defined in your new code? In simple terms, the new warning you are getting suggests that the species in `frogtree.2` and `dat` do not match. That is, ggtree doesn't know how to plot the point representing species A if species A is not labeld on the tree. You can start to diagnose with something like `setdiff(dat$SPECIES, frogtree.2$tip.label)`. Cool plot by the way!! – Skaqqs Aug 09 '21 at 15:28
  • After a long and tedious journey, it all came down to a few opposing capital letters and spaces between my DF and tree. I am finally happy with it, thank you so much for your help! Probably would have given up a long time ago. :) – Shannon Rae Aug 18 '21 at 16:38