Quitting from lines 43-67 (treedata.Rmd)
Error in mypkg("Archaeopteryx", "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx") :
没有"mypkg"这个函数
Calls: render_book ... eval -> eval -> source -> withVisible -> eval -> eval

??mypkg
yulab.utils::get_fun_from_pkg
get_fun_from_pkg
Aliases: get_fun_from_pkg

I was trying to reproduce example from the Chapter 9.2: ggtree for dendrograms:

hc <- hclust(dist(mtcars))
p <- ggtree(hc)

It gives an error:

Error: `data` must be a data frame, or other object coercible by `fortify()`, not an S3 object with class hclust
Run `rlang::last_error()` to see where the error occurred.

Hello. I have the following versions installed

• ggtree: ‘2.3.0.991’
• treeio: ‘1.13.0’
• tidytree: ‘0.3.3’

but I'm still getting the following error

Error in UseMethod("nodeid"): no applicable method for 'nodeid' applied to an object of class "phylo"

when running the example in 4.3.5:

library(ggtree)
library(treeio)
library(tidytree)

anole.tree<-read.tree("http://www.phytools.org/eqg2015/data/anole.tre")
svl <- read.csv("http://www.phytools.org/eqg2015/data/svl.csv",
    row.names=1)
svl <- as.matrix(svl)[,1]
fit <- phytools::fastAnc(anole.tree,svl,vars=TRUE,CI=TRUE)

td <- data.frame(node = nodeid(anole.tree, names(svl)),
               trait = svl)
nd <- data.frame(node = names(fit$ace), trait = fit$ace)

d <- rbind(td, nd)
d$node <- as.numeric(d$node)
tree <- full_join(anole.tree, d, by = 'node')

ggtree(tree, aes(color=trait), layout = 'circular', 
        ladderize = FALSE, continuous = TRUE, size=2) +
    scale_color_gradientn(colours=c("red", 'orange', 'green', 'cyan', 'blue')) +
    geom_tiplab(hjust = -.1) + xlim(0, 1.2) + theme(legend.position = c(.05, .85)) 

How can I fix this?

Hi Professor Yu.

I am always being a fan of ggtree, and try to used it whenever I can.
I was trying to use the ylim2() function to plot my tree with other plot next to it. However, ylim2 doesn't appear in the ggtree package. I am using the ggtree version 2.0.1.

Maybe I am looking in the wrong direction. Thank you for the help and this great package!.

Melody

EDIT: I found the newest version. I was using the old one. As I though, I was looking in the wrong direction. Thank you for your constantly effort in this amazing package!

Hi @GuangchuangYu,

I was following along in your treedata-book to refresh my ggtree-skills. Thank you for this very valuable resource.

During this read, I stumbled on the layer function geom_hilight (Chapter 4), which is used to highlight a clade. However, I believe that geom_hilight is misspelled and should be changed to geom_highlight. See for example this recourse.

Thank you for considering this change and the development of the packages.

Regards,
Sander

Hey Yu,

Thanks for your great job on ggtree.
I wanna change the position of geom_balance but there's no positional arg. Is it possible to solve it?

Best,
Yun

The issue line [aplot::plot_list(p1, p2, tag_levels = "A", widths = c(0.6, 0.4))
](

I already tried remotes::install_github("YuLab-SMU/aplot")

Quitting from lines 5778-5786 (treedata.Rmd)
Error: No method for merging list into element_text
Backtrace:
     █
  1. ├─bookdown::render_book("index.Rmd", "bs4_book")
  2. │ └─bookdown:::render_cur_session(...)
  3. │   └─rmarkdown::render(main, output_format, ..., clean = clean, envir = envir)
  4. │     └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
  5. │       └─knitr:::process_file(text, output)
  6. │         ├─base::withCallingHandlers(...)
  7. │         ├─knitr:::process_group(group)
  8. │         └─knitr:::process_group.block(group)
  9. │           └─knitr:::call_block(x)
 10. │             └─knitr:::block_exec(params)
 11. │               └─knitr:::eng_r(options)
 12. │                 ├─knitr:::in_dir(...)
 13. │                 └─knitr:::evaluate(...)
 14. │                   └─evaluate::evaluate(...)
 15. │                     └─evaluate:::evaluate_call(...)
 16. │                       ├─evaluate:::timing_fn(...)
 17. │                       ├─base:::handle(...)
 18. │                       ├─base::withCallingHandlers(...)
 19. │                       ├─base::withVisible(eval(expr, envir, enclos))
 20. │                       └─base::eval(expr, envir, enclos)
 21. │                         └─base::eval(expr, envir, enclos)
 22. └─aplot::plot_list(p1, p2, tag_levels = "A", widths = c(0.6, 0.4))
 23.   └─patchwork:::`&.gg`(...)
 24.     └─base::lapply(...)
 25.       └─patchwork:::FUN(X[[i]], ...)
 26.         └─ggplot2:::`+.gg`(p, e2)
 27.           └─ggplot2:::add_ggplot(e1, e2, e2name)
 28.             ├─ggplot2::ggplot_add(object, p, objectname)
 29.             └─ggplot2:::ggplot_add.theme(object, p, objectname)
 30.               └─ggplot2:::add_theme(plot$theme, object)
 31.                 ├─ggplot2::merge_element(t2[[item]], t1[[item]])
 32.                 └─ggplot2:::merge_element.default(t2[[item]], t1[[item]])
 33. ```

Hi @GuangchuangYu, I see that this is a book concerning an rOpenSci package and was therefore wondering whether you'd like to transfer it to the ropensci-books organization.

E.g. drake manual https://github.com/ropensci-books/drake with the rendered book in the gh-pages branch

URL https://books.ropensci.org/drake/

The advantages are getting such a pretty URL and being listed in https://books.ropensci.org/ You'd retain admin rights on your book repo.

There's absolutely no obligation!

cc @jeroen (who set up the ropensci-books org)

Hi,
I found your treedata-book and found it useful.

Although, as I am new to R and what I usually find most irritating when looking at examples of different code is that the input file is never posted. My input file, for example a csv with SNP data may look different to the one you use depending on what you've used to generate the SNP data with.

What I think would be great is to actually show what your input files that you use in your different examples look like. Even better if you would want to include the files that you've used in your examples and then a new user could try and replicate using your files first before moving onto their own files!

Great book though!

Dear Guangchuang Yu,

Your book on ggtree is amazing! It helped me a lot to make nice figures. Many thanks for making this openly available.

One thing I would recommend is to change the colour scheme in Figure 4.14. This figure is impossible to read for colourblind people. Having a colour gradient from dark green to red looks completely homogeneous to colourblind people. It would be great if you could change that so that people using your book will not copy the example and propagate the use of colour schemes that are not colourblind-save. Else, most figures I looked at are beautiful and mostly colourblind save.

Best,
Joana

Hi,

I was trying to plot an ML tree with data based on the example here:https://yulab-smu.top/treedata-book/chapter7.html#ggtree_object , chapter: 7.1 mapping data to the tree strucutre

And to start, I was following the script that is given in the webpage but I’m getting errors, it seems not to recognize my metadata.

I am attaching the tree and the metadata and my code .

Can you help me?

Thank you,

Carla

tree.nwk

(Miami_VP01-BL-D-4Seq-1_Freq_31.4546304957905:0.0391764546,((((((((Miami_VP01-BL-D-4Seq-2_Freq_7.97474275023386:0.0180673245,(Miami_VP01-BL-D-4Seq-4_Freq_7.20299345182413:0.0288746301,Miami_VP01-BL-D-4Seq-7_Freq_3.99906454630496:0.0093703420)100:0.0186559944)98:0.0106905559,Miami_VP01-BL-D-4Seq-5_Freq_5.00467726847521:0.0204139776)92:0.0102525246,(Miami_VP01-BL-D-4Seq-3_Freq_14.9672591206735:0.0233094297,Miami_VP01-BL-D-4Seq-6_Freq_4.09260991580917:0.0116586417)94:0.0125728907)71:0.0019297308,(((Miami_VP01-R-3Seq-1_Freq_40.9963116858864:0.0080173189,(Miami_VP01-R-3Seq-4_Freq_10.6494234091227:0.0061503988,Miami_VP01-R-3Seq-5_Freq_4.99556468555955:0.0144382491)80:0.0018165748)52:0.0000010000,((Miami_VP01-R-3Seq-2_Freq_8.14230356225781:0.0079434585,Miami_VP01-R-3Seq-3_Freq_21.1261029926701:0.0059381860)42:0.0000010000,Miami_VP01-R-3Seq-6_Freq_4.38862692002428:0.0039596553)31:0.0000010000)50:0.0000010000,Miami_VP01-R-3Seq-7_Freq_2.59582613567393:0.0182658096)74:0.0022617194)88:0.0076715780,Miami_VP01-R-3Seq-8_Freq_3.4035202390401:0.0000010000)81:0.0019624401,Miami_VP01-R-3Seq-9_Freq_3.69298286568:0.0039527218)96:0.0169191950,(((((((Miami_VP01-BL-R-1Seq-1_Freq_24.7746243739566:0.0085585132,Miami_VP01-BL-R-1Seq-2_Freq_6.91151919866444:0.0042164778)28:0.0000010000,Miami_VP01-BL-R-1Seq-6_Freq_16.974958263773:0.0020997551)6:0.0000010000,(Miami_VP01-BL-R-1Seq-4_Freq_3.87312186978297:0.0000010000,Miami_VP01-BL-R-1Seq-5_Freq_5.66944908180301:0.0000010000)65:0.0000010000)5:0.0000010000,(Miami_VP01-BL-R-1Seq-7_Freq_27.7529215358932:0.0042320651,Miami_VP01-BL-R-1Seq-8_Freq_2.43739565943239:0.0020956728)27:0.0000010000)28:0.0000010000,Miami_VP01-BL-R-1Seq-3_Freq_7.18530884808013:0.0063358778)82:0.0018083868,Miami_VP01-BL-R-1Seq-9_Freq_4.41402337228715:0.0045438562)100:0.0616779797,(((((Miami_VP01-R-2Seq-1_Freq_29.8493267257346:0.0282875513,Miami_VP01-R-2Seq-9_Freq_7.49361766030936:0.0044904112)81:0.0018040480,((Miami_VP01-R-2Seq-2_Freq_9.83130600190219:0.0019812472,Miami_VP01-R-2Seq-6_Freq_8.52980928067277:0.0084323992)90:0.0063325096,Miami_VP01-R-2Seq-4_Freq_5.57140711818591:0.0061799056)44:0.0000010000)61:0.0000010000,(Miami_VP01-R-2Seq-3_Freq_8.99033888972318:0.0125674004,Miami_VP01-R-2Seq-5_Freq_21.3445462281624:0.0147813306)67:0.0019949554)89:0.0084176437,Miami_VP01-R-2Seq-7_Freq_5.03579115983381:0.0040679009)84:0.0104814500,Miami_VP01-R-2Seq-8_Freq_3.34885117885568:0.0134109984)81:0.0051375462)95:0.0142570091)93:0.0110711000,Miami_VP01-BL-D-4Seq-8_Freq_13.4471468662301:0.0042512688)57:0.0012129753,Miami_VP01-BL-D-4Seq-9_Freq_11.8334892422825:0.0093601630);

metadata.csv

name,condition,frequency
Miami_VP01-BL-D-4Seq-1_Freq:31.4546304957905,Baseline DNA,31.5
Miami_VP01-BL-D-4Seq-2_Freq:7.97474275023386,Baseline DNA,8
Miami_VP01-BL-D-4Seq-3_Freq:14.9672591206735,Baseline DNA,15
Miami_VP01-BL-D-4Seq-4_Freq:7.20299345182413,Baseline DNA,7.2
Miami_VP01-BL-D-4Seq-5_Freq:5.00467726847521,Baseline DNA,5
Miami_VP01-BL-D-4Seq-6_Freq:4.09260991580917,Baseline DNA,4.1
Miami_VP01-BL-D-4Seq-7_Freq:3.99906454630496,Baseline DNA,4
Miami_VP01-BL-D-4Seq-8_Freq:13.4471468662301,Baseline DNA,13.4
Miami_VP01-BL-D-4Seq-9_Freq:11.8334892422825,Baseline DNA,11.8
Miami_VP01-BL-R-1Seq-1_Freq:24.7746243739566,Baseline RNA,24.8
Miami_VP01-BL-R-1Seq-2_Freq:6.91151919866444,Baseline RNA,6.9
Miami_VP01-BL-R-1Seq-3_Freq:7.18530884808013,Baseline RNA,7.2
Miami_VP01-BL-R-1Seq-4_Freq:3.87312186978297,Baseline RNA,3.9
Miami_VP01-BL-R-1Seq-5_Freq:5.66944908180301,Baseline RNA,5.7
Miami_VP01-BL-R-1Seq-6_Freq:16.974958263773,Baseline RNA,17
Miami_VP01-BL-R-1Seq-7_Freq:27.7529215358932,Baseline RNA,27.8
Miami_VP01-BL-R-1Seq-8_Freq:2.43739565943239,Baseline RNA,2.4
Miami_VP01-BL-R-1Seq-9_Freq:4.41402337228715,Baseline RNA,4.4
Miami_VP01-R-2Seq-1_Freq:29.8493267257346,After culture no co-culture RNA,29.8
Miami_VP01-R-2Seq-2_Freq:9.83130600190219,After culture no co-culture RNA,9.8
Miami_VP01-R-2Seq-3_Freq:8.99033888972318,After culture no co-culture RNA,9
Miami_VP01-R-2Seq-4_Freq:5.57140711818591,After culture no co-culture RNA,5.6
Miami_VP01-R-2Seq-5_Freq:21.3445462281624,After culture no co-culture RNA,21.3
Miami_VP01-R-2Seq-6_Freq:8.52980928067277,After culture no co-culture RNA,8.5
Miami_VP01-R-2Seq-7_Freq:5.03579115983381,After culture no co-culture RNA,5
Miami_VP01-R-2Seq-8_Freq:3.34885117885568,After culture no co-culture RNA,3.3
Miami_VP01-R-2Seq-9_Freq:7.49361766030936,After culture no co-culture RNA,7.5
Miami_VP01-R-3Seq-1_Freq:40.9963116858864,After culture co-culture RNA,41
Miami_VP01-R-3Seq-2_Freq:8.14230356225781,After culture co-culture RNA,8.1
Miami_VP01-R-3Seq-3_Freq:21.1261029926701,After culture co-culture RNA,21.1
Miami_VP01-R-3Seq-4_Freq:10.6494234091227,After culture co-culture RNA,10.6
Miami_VP01-R-3Seq-5_Freq:4.99556468555955,After culture co-culture RNA,5
Miami_VP01-R-3Seq-6_Freq:4.38862692002428,After culture co-culture RNA,4.4
Miami_VP01-R-3Seq-7_Freq:2.59582613567393,After culture co-culture RNA,2.6
Miami_VP01-R-3Seq-8_Freq:3.4035202390401,After culture co-culture RNA,3.4
Miami_VP01-R-3Seq-9_Freq:3.69298286568,After culture co-culture RNA,3.7

CODE

library(ggtree)
x <- read.tree("tree.nwk")
info <- read.csv("metadata.csv")
p <- ggtree(x) %<+% info + xlim(-.1, 4)
plot(p)
p2 <- p +
geom_tippoint(aes(shape = condition, color = condition, size = frequency) +
theme(legend.position = "right")) #+ scale_size_continuous(range = c(3, 10)))

plot(p2)

Reading through Chapter 4, I can't seem to get geom_tree(ladderize = F) working, reprex:

library("treeio")
#> treeio v1.10.0  For help: https://yulab-smu.github.io/treedata-book/

library("ggtree")
#> ggtree v2.0.1  For help: https://yulab-smu.github.io/treedata-book/

nwk <- system.file("extdata", "sample.nwk", package="treeio")
tree <- read.tree(nwk)

ggplot(tree, aes(x, y)) + geom_tree(ladderize = F) + theme_tree()
#> Warning: Ignoring unknown parameters: ladderize
#> Warning: Ignoring unknown parameters: ladderize

Hi Guangchuang,

I have updated everything to the latest versions, and sorry the code is still not working:

ggtree version 2.2.4

R.version
_
platform x86_64-apple-darwin17.0
arch x86_64
os darwin17.0
system x86_64, darwin17.0
status
major 4
minor 0.2
year 2020
month 06
day 22
svn rev 78730
language R
version.string R version 4.0.2 (2020-06-22)
nickname Taking Off Again

## using external data
d <- data.frame(node=c(17, 21), type=c("A", "B"))
ggtree(tree) + geom_hilight(data=d, aes(node=node, fill=type))

Error in (function (node, mapping = NULL, fill = "steelblue", alpha = 0.5,  : 
  unused argument (data = list(c(17, 21), c("A", "B")))

## using data stored in tree object
x <- read.nhx(system.file("extdata/NHX/ADH.nhx", package="treeio"))
ggtree(x) + geom_hilight(mapping=aes(subset = node %in% c(10, 12), fill = S)) +
  scale_fill_manual(values=c("steelblue", "darkgreen"))

Error in structure(list(node = node, fill = fill, alpha = alpha, extend = extend,  : 
  argument "node" is missing, with no default

Could you please shed any light on why my code is not working?

Many thanks!

Dear Dr.Yu
I am using your wonderful tree-book to create a figure for a paper. I look forward to your response to this question.

#Question:
I received a Warning message when I tried to retrieve PhyloPics from the database.

Error in download_url(path) :
Failed to download http://phylopic.org/assets/images/submissions/7e9286b9-0e49-46c2-88f6-218291fb06a4.512.png (HTTP 404)

I used the code below:

newick <- "(Homo_sapiens:0.029752,(((Xenopus_tropicalis:0.096645,Caenorhabditis_elegans:0.647764):0.030884,Danio_rerio:0.100106):0.064097,Gallus_gallus:0.029353):0.024960,Mus_musculus:0.018171);"

tree <- read.tree(text=newick)

d <- ggimage::phylopic_uid(tree$tip.label)

ggtree(tree) %<+% d + geom_tiplab(aes(image=uid), geom="phylopic", offset=2.5) + geom_tiplab(aes(label=label), offset = .2) + xlim(NA, 7) + scale_color_viridis_d()

The "Using external data" section has code to highlight clades and make a legend (figures 5.4 E and F).

However this code does not work:

## using external data
d <- data.frame(node=c(17, 21), type=c("A", "B"))
ggtree(tree) + geom_hilight(data=d, aes(node=node, fill=type))

I get an error saying:

Error in (function (node, mapping = NULL, fill = "steelblue", alpha = 0.5,  : 
  unused argument (data = list(c(17, 21), 1:2))

geom_hilight() does not take the argument 'data'.

When I also run this code:

x <- read.nhx(system.file("extdata/NHX/ADH.nhx", package="treeio"))
ggtree(x) + geom_hilight(mapping=aes(subset = node %in% c(10, 12), fill = S)) +
  scale_fill_manual(values=c("steelblue", "darkgreen"))

I get a similar error:

Error in structure(list(node = node, fill = fill, alpha = alpha, extend = extend,  : 
  argument "node" is missing, with no default

既然geom_cladelab是更好的实现，那么应该把书里的内容更新一下。