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YuLab-SMU / ggtree

:christmas_tree:Visualization and annotation of phylogenetic trees
https://yulab-smu.top/treedata-book/
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The problem about the tree display #456

Open hansir8 opened 2 years ago

hansir8 commented 2 years ago

Dear Professor Yu, Here, we constructed a phylogenetic tree using the neighbor-joining method in MEGA (command line version 11.0.10 ), including 3847 genomic sequences (attached tree file 1 tree1.nwk.zip). The exported tree was correctly displayed in the FigTree software (v1.4.4), and we reset the midpoint-rooted phylogenetic tree in FigTree software (attached figure 1 figture 1). When the tree file was read in ggtree, we meet a problem about the phylogenetic tree shape (attached figture 2figture 2). Some lineages in the phylogenetic tree are aggregated, but the tree in FigTree software is correct. We tried some methods to solve this problem, we read the original tree file output by MEGA (attached tree file 2tree2.nwk.zip); read the tree file in other format in ggtree. However, the same problem appeared in the end. We used the IQtree to constructed a ML tree, the results were correct. We suspect some sequences are identical in the tree, which cause this problem. But we need the neighbor-joining method to construct a tree for personal usage. Is there any solution for this?

The code we used: library(ggtree)

ggtree v3.3.0.900---

 tree <- read.newick(file = "tree.nwk")
 ggtree(tree)
      ##Warning message:
      ##In fortify.phylo(data, ...) : 'edge.length' contains NA values...
       ## setting 'edge.length' to NULL automatically when plotting the tree...
brj1 commented 2 years ago

This is a bug in the package, ape (read.tree / read.newick use ape to read the tree). It is fixed in the development version of ape. Install that version via:

install.packages("remotes")
remotes::install_github("emmanuelparadis/ape")
hansir8 commented 2 years ago

Thanks for your reply! I try this solution, but an error appeared. I suspect that it was caused by basic packages compatibility。

The machine: MAC OS 10.14.6

R.version _
platform x86_64-apple-darwin17.0
arch x86_64
os darwin17.0
system x86_64, darwin17.0
status
major 4
minor 0.3
year 2020
month 10
day 10
svn rev 79318
language R
version.string R version 4.0.3 (2020-10-10) nickname Bunny-Wunnies Freak Out

The commang line I used:

remotes::install_github("emmanuelparadis/ape") Downloading GitHub repo emmanuelparadis/ape@HEAD ✓ checking for file ‘/private/var/folders/_x/3nw9jqsn5jvgm4x8kzl317pw0000gn/T/Rtmpis2WOm/remotes139a74aff76a0/emmanuelparadis-ape-decfeac/DESCRIPTION’ ... ─ preparing ‘ape’: ✓ checking DESCRIPTION meta-information ... ─ cleaning src ─ installing the package to process help pages

─ installing source package ‘ape’ ... using staged installation libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c BIONJ.c -o BIONJ.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c NNI.c -o NNI.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c RcppExports.cpp -o RcppExports.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c SPR.c -o SPR.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c additive.c -o additive.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c ape.c -o ape.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c bNNI.c -o bNNI.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c bionjs.c -o bionjs.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c bipartition.c -o bipartition.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c bitsplits.c -o bitsplits.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c delta_plot.c -o delta_plot.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c dist_dna.c -o dist_dna.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c dist_nodes.c -o dist_nodes.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c ewLasso.c -o ewLasso.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c heap.c -o heap.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c mat_expo.c -o mat_expo.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c me.c -o me.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c me_balanced.c -o me_balanced.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c me_ols.c -o me_ols.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c mvr.c -o mvr.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c mvrs.c -o mvrs.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c nj.c -o nj.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c njs.c -o njs.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c pic.c -o pic.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c plot_phylo.c -o plot_phylo.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c prop_part.cpp -o prop_part.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c rTrait.c -o rTrait.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c read_dna.c -o read_dna.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c reorder_Rcpp.cpp -o reorder_Rcpp.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c reorder_phylo.c -o reorder_phylo.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c treePop.c -o treePop.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c tree_build.c -o tree_build.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c tree_phylo.c -o tree_phylo.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c triangMtd.c -o triangMtd.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c triangMtds.c -o triangMtds.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c ultrametric.c -o ultrametric.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ape.so BIONJ.o NNI.o RcppExports.o SPR.o additive.o ape.o bNNI.o bionjs.o bipartition.o bitsplits.o delta_plot.o dist_dna.o dist_nodes.o ewLasso.o heap.o mat_expo.o me.o me_balanced.o me_ols.o mvr.o mvrs.o nj.o njs.o pic.o plot_phylo.o prop_part.o rTrait.o read_dna.o reorder_Rcpp.o reorder_phylo.o treePop.o tree_build.o tree_phylo.o triangMtd.o triangMtds.o ultrametric.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0' ld: warning: directory not found for option '-L/usr/local/gfortran/lib' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [ape.so] Error 1 ERROR: compilation failed for package ‘ape’ ─ removing ‘/private/var/folders/_x/3nw9jqsn5jvgm4x8kzl317pw0000gn/T/Rtmpy8kDxF/Rinst15b5b6da9ff30/ape’

ERROR: package installation failed 错误: Failed to install 'ape' from GitHub: System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines): E> clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ape.so BIONJ.o NNI.o RcppExports.o SPR.o additive.o ape.o bNNI.o bionjs.o bipartition.o bitsplits.o delta_plot.o dist_dna.o dist_nodes.o ewLasso.o heap.o mat_expo.o me.o me_balanced.o me_ols.o mvr.o mvrs.o nj.o njs.o pic.o plot_phylo.o prop_part.o rTrait.o read_dna.o reorder_Rcpp.o reorder_phylo.o treePop.o tree_build.o tree_phylo.o triangMtd.o triangMtds.o ultrametric.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framewor

GuangchuangYu commented 2 years ago

You can use rhub::check_on_macos() to help build the package from the source tarball, and then download the binary file from rhub to install.

hansir8 commented 2 years ago

Thanks for your reply! Professor Yu. I am trying this solution, and the installation of ape package is proceeding, but it is not complete till now. If it work, I will feedback. Thanks again!

hansir8 commented 2 years ago

It is solved in the newest version of ape (5.6 and later).