#ggtree has a relatively steep learning curve. But after looking at a few Python alternatives eg., toytree, ETE, Bio.Phylo it's hard to match its layout versatility. 21 tree variants with just a few lines of code.
#rstats #phylogenetics #bioinformatics
#rstats #phylogenetics #bioinformatics
March 12, 2026 at 8:34 PM
#ggtree has a relatively steep learning curve. But after looking at a few Python alternatives eg., toytree, ETE, Bio.Phylo it's hard to match its layout versatility. 21 tree variants with just a few lines of code.
#rstats #phylogenetics #bioinformatics
#rstats #phylogenetics #bioinformatics
Label or collapse nodes in ggtree phylogenies iteratively with purrr::reduce
brief new R post
luisdva.github.io/rstats/reduc...
brief new R post
luisdva.github.io/rstats/reduc...
April 25, 2024 at 6:36 PM
Label or collapse nodes in ggtree phylogenies iteratively with purrr::reduce
brief new R post
luisdva.github.io/rstats/reduc...
brief new R post
luisdva.github.io/rstats/reduc...
Pleased to see our work published:
The Ties That Bind: Computational, Cross-cultural Analyses of Knots Reveal Their Cultural Evolutionary History and Significance
We analysed knots across 12,000 years and 82 societies.
Time to tie a thread 🧵 about why knots matter.
doi.org/10.1017/S095...
The Ties That Bind: Computational, Cross-cultural Analyses of Knots Reveal Their Cultural Evolutionary History and Significance
We analysed knots across 12,000 years and 82 societies.
Time to tie a thread 🧵 about why knots matter.
doi.org/10.1017/S095...
March 13, 2025 at 12:41 PM
Pleased to see our work published:
The Ties That Bind: Computational, Cross-cultural Analyses of Knots Reveal Their Cultural Evolutionary History and Significance
We analysed knots across 12,000 years and 82 societies.
Time to tie a thread 🧵 about why knots matter.
doi.org/10.1017/S095...
The Ties That Bind: Computational, Cross-cultural Analyses of Knots Reveal Their Cultural Evolutionary History and Significance
We analysed knots across 12,000 years and 82 societies.
Time to tie a thread 🧵 about why knots matter.
doi.org/10.1017/S095...
The cool things about ggtree don't stop here. You can use geom_text() or geom_label() to display node and tip labels simultaneously, or geom_tiplab() to show only tip labels. You can even have nodes and tips looking differently
#ggtree #rstats #phylogenetics #dataviz #bioinformatics #ggplot2
#ggtree #rstats #phylogenetics #dataviz #bioinformatics #ggplot2
March 15, 2026 at 9:50 PM
The cool things about ggtree don't stop here. You can use geom_text() or geom_label() to display node and tip labels simultaneously, or geom_tiplab() to show only tip labels. You can even have nodes and tips looking differently
#ggtree #rstats #phylogenetics #dataviz #bioinformatics #ggplot2
#ggtree #rstats #phylogenetics #dataviz #bioinformatics #ggplot2
I learned how to use ggtreeExtra this week for phylogeny visualization and annotation.
ggtree: yulab-smu.top/treedata-book/
ggtreeExtra: bioconductor.org/packages/dev...
ggtree: yulab-smu.top/treedata-book/
ggtreeExtra: bioconductor.org/packages/dev...
December 7, 2023 at 1:44 AM
I learned how to use ggtreeExtra this week for phylogeny visualization and annotation.
ggtree: yulab-smu.top/treedata-book/
ggtreeExtra: bioconductor.org/packages/dev...
ggtree: yulab-smu.top/treedata-book/
ggtreeExtra: bioconductor.org/packages/dev...
Scalable method for exploring #phylogenetic placement uncertainty with custom #visualizations using #treeio and #ggtree onlinelibrary.wiley.com/doi/full/10....
#ggplot2 #R #Rstudio #Bioinformatics
#ggplot2 #R #Rstudio #Bioinformatics
Scalable method for exploring phylogenetic placement uncertainty with custom visualizations using treeio and ggtree
The treeio and ggtree packages provide robust tools for the comprehensive parsing and visualization of phylogenetic placement data. These tools enable detailed analyses, including placement filtratio...
onlinelibrary.wiley.com
January 20, 2025 at 10:29 AM
Scalable method for exploring #phylogenetic placement uncertainty with custom #visualizations using #treeio and #ggtree onlinelibrary.wiley.com/doi/full/10....
#ggplot2 #R #Rstudio #Bioinformatics
#ggplot2 #R #Rstudio #Bioinformatics
Here is a short example of how to create a phylogenetic tree like the one on the left. I use data and silhouettes provided by the ggtree package — more is coming in the next days!
#ggtree #rstats #phylogenetics #dataviz #bioinformatics #ggplot2 #PhyloPic code: gist.github.com/loukesio/dd3...
#ggtree #rstats #phylogenetics #dataviz #bioinformatics #ggplot2 #PhyloPic code: gist.github.com/loukesio/dd3...
March 15, 2026 at 10:54 PM
Here is a short example of how to create a phylogenetic tree like the one on the left. I use data and silhouettes provided by the ggtree package — more is coming in the next days!
#ggtree #rstats #phylogenetics #dataviz #bioinformatics #ggplot2 #PhyloPic code: gist.github.com/loukesio/dd3...
#ggtree #rstats #phylogenetics #dataviz #bioinformatics #ggplot2 #PhyloPic code: gist.github.com/loukesio/dd3...
thats a very interesting phylogenetic tree that reflect the avian evolution. I know its a big jump, but can we build something like this with #ggtree ?
www.nature.com/articles/s41...
www.nature.com/articles/s41...
March 15, 2026 at 10:11 PM
thats a very interesting phylogenetic tree that reflect the avian evolution. I know its a big jump, but can we build something like this with #ggtree ?
www.nature.com/articles/s41...
www.nature.com/articles/s41...
💬 "There’s already plenty of documentation out there for how to use #ggtree, but there is the odd thing I come up against that I haven’t seen explicitly demonstrated before." - @rowenahill.bsky.social.
A guide to plotting #phylogenetictrees in #R, and automating clade highlights
buff.ly/Vd5b61a
🧬💻
A guide to plotting #phylogenetictrees in #R, and automating clade highlights
buff.ly/Vd5b61a
🧬💻
Plotting phylogenetic trees in R: alternating clade highlights
A guide to highlighting clades in phylogenetic trees in R
buff.ly
August 1, 2025 at 11:01 AM
💬 "There’s already plenty of documentation out there for how to use #ggtree, but there is the odd thing I come up against that I haven’t seen explicitly demonstrated before." - @rowenahill.bsky.social.
A guide to plotting #phylogenetictrees in #R, and automating clade highlights
buff.ly/Vd5b61a
🧬💻
A guide to plotting #phylogenetictrees in #R, and automating clade highlights
buff.ly/Vd5b61a
🧬💻
#ggtree by @yulab.bsky.social is fantastic for visualizing #phylo data in @rconsortium.bsky.social as it’s mounted on the @posit.co tidyverse. These are some phylopic.org homework plots from the #sistematicaunam class at @ib_unam real purdy ain’t ‘em?
March 18, 2026 at 7:32 PM
#ggtree by @yulab.bsky.social is fantastic for visualizing #phylo data in @rconsortium.bsky.social as it’s mounted on the @posit.co tidyverse. These are some phylopic.org homework plots from the #sistematicaunam class at @ib_unam real purdy ain’t ‘em?
From the upcoming #AppsPlantSci Phylogenetic Networks issue
tanggle: An R package for the visualization of #phylogenetic networks (by Schliep, Vidal-Garcia, Solis-Lemus, et al)
bsapubs.onlinelibrary.wiley.com/doi/full/10.... @uwdsi.bsky.social #Rpackage #ggtree #macroevolution #evolution
tanggle: An R package for the visualization of #phylogenetic networks (by Schliep, Vidal-Garcia, Solis-Lemus, et al)
bsapubs.onlinelibrary.wiley.com/doi/full/10.... @uwdsi.bsky.social #Rpackage #ggtree #macroevolution #evolution
June 4, 2026 at 3:34 PM
From the upcoming #AppsPlantSci Phylogenetic Networks issue
tanggle: An R package for the visualization of #phylogenetic networks (by Schliep, Vidal-Garcia, Solis-Lemus, et al)
bsapubs.onlinelibrary.wiley.com/doi/full/10.... @uwdsi.bsky.social #Rpackage #ggtree #macroevolution #evolution
tanggle: An R package for the visualization of #phylogenetic networks (by Schliep, Vidal-Garcia, Solis-Lemus, et al)
bsapubs.onlinelibrary.wiley.com/doi/full/10.... @uwdsi.bsky.social #Rpackage #ggtree #macroevolution #evolution
I can’t tell if this is completely insane or not…but I’m making it so that every data figure in every paper of mine going forward is reproducible by anyone. Claude helping me figure out how to fine tune R scripts (and specifically ggtree for phylogenies) has been kind of critical
June 13, 2026 at 2:35 PM
I can’t tell if this is completely insane or not…but I’m making it so that every data figure in every paper of mine going forward is reproducible by anyone. Claude helping me figure out how to fine tune R scripts (and specifically ggtree for phylogenies) has been kind of critical
💬 "There’s already plenty of documentation out there for how to use #ggtree, but there is the odd thing I come up against that I haven’t seen explicitly demonstrated before."
A guide to plotting #phylogenetictrees in #R, and automating clade highlights, by @rowenahill.bsky.social 👇
A guide to plotting #phylogenetictrees in #R, and automating clade highlights, by @rowenahill.bsky.social 👇
Plotting phylogenetic trees in R: alternating clade highlights
A guide to highlighting clades in phylogenetic trees in R
buff.ly
February 17, 2025 at 12:00 PM
💬 "There’s already plenty of documentation out there for how to use #ggtree, but there is the odd thing I come up against that I haven’t seen explicitly demonstrated before."
A guide to plotting #phylogenetictrees in #R, and automating clade highlights, by @rowenahill.bsky.social 👇
A guide to plotting #phylogenetictrees in #R, and automating clade highlights, by @rowenahill.bsky.social 👇
I SWEAR ggtree will be the cause of my high blood pressure.
January 14, 2025 at 6:05 AM
I SWEAR ggtree will be the cause of my high blood pressure.
I'm going with ggtree and ggtreeextra, steep learning curve (in my experience) but worth it I feel bioconductor.org/packages/dev....
I know others were happy with ete toolkit
I know others were happy with ete toolkit
ggtree: tree visualization and annotation
bioconductor.org
May 20, 2024 at 6:17 PM
I'm going with ggtree and ggtreeextra, steep learning curve (in my experience) but worth it I feel bioconductor.org/packages/dev....
I know others were happy with ete toolkit
I know others were happy with ete toolkit
One thing this workflow can easily adapt is appending a cladogram (using ggtree: guangchuangyu.github.io/software/ggt...) to the left of the synteny graphics, and reorder the y axis to match the y axis of the species tree.
A workflow for Tidyverse-based local synteny visualization: Good for visualizing local synteny across species, genotypes, or acorss regions of a genome. Can be used to showcase copy number variation. Still need to write the tutorial, but will be on my GitHub soon. #Genomics #DataVisualization
December 11, 2024 at 1:04 AM
One thing this workflow can easily adapt is appending a cladogram (using ggtree: guangchuangyu.github.io/software/ggt...) to the left of the synteny graphics, and reorder the y axis to match the y axis of the species tree.
To flip the axis, you can use revts() on the ggtree object, then set the x axis scale AFTER. You'll need to account for the fact that the x limits/breaks will be - values and use absolute value on the labels.
p <- ggtree(tr) + theme_tree2()
p2 <- revts(p) + scale_x_continuous(labels=abs)
p <- ggtree(tr) + theme_tree2()
p2 <- revts(p) + scale_x_continuous(labels=abs)
February 5, 2025 at 2:00 PM
To flip the axis, you can use revts() on the ggtree object, then set the x axis scale AFTER. You'll need to account for the fact that the x limits/breaks will be - values and use absolute value on the labels.
p <- ggtree(tr) + theme_tree2()
p2 <- revts(p) + scale_x_continuous(labels=abs)
p <- ggtree(tr) + theme_tree2()
p2 <- revts(p) + scale_x_continuous(labels=abs)
📢 deeptime: an R package that facilitates highly customizable and reproducible visualizations of data over geological time intervals
🔗 doi.org/10.1080/2096...
Fully #openaccess in @bigearthdata1.bsky.social with insight about deeptime📦 development and code examples!
#rstats #geology #paleontology
🔗 doi.org/10.1080/2096...
Fully #openaccess in @bigearthdata1.bsky.social with insight about deeptime📦 development and code examples!
#rstats #geology #paleontology
August 6, 2025 at 1:06 PM
📢 deeptime: an R package that facilitates highly customizable and reproducible visualizations of data over geological time intervals
🔗 doi.org/10.1080/2096...
Fully #openaccess in @bigearthdata1.bsky.social with insight about deeptime📦 development and code examples!
#rstats #geology #paleontology
🔗 doi.org/10.1080/2096...
Fully #openaccess in @bigearthdata1.bsky.social with insight about deeptime📦 development and code examples!
#rstats #geology #paleontology
Molecular biologists are especially interested in domains and motifs with known functions. BAT can highlight user-provided HMM profiles and amino acid motifs (via the ggtree R package) to visualize these features on a gene tree. Domain gain/loss is placed in evolutionary context.
May 13, 2026 at 12:22 AM
Molecular biologists are especially interested in domains and motifs with known functions. BAT can highlight user-provided HMM profiles and amino acid motifs (via the ggtree R package) to visualize these features on a gene tree. Domain gain/loss is placed in evolutionary context.
Styling ggtree branches is easy; change color, linewidth, and linetype directly inside the ggtree() call. Works the same across rectangular, circular, and slanted layouts. Colors from the alger palette (ltc package).
#ggtree #rstats #phylogenetics #dataviz
#ggtree #rstats #phylogenetics #dataviz
March 15, 2026 at 9:54 PM
Styling ggtree branches is easy; change color, linewidth, and linetype directly inside the ggtree() call. Works the same across rectangular, circular, and slanted layouts. Colors from the alger palette (ltc package).
#ggtree #rstats #phylogenetics #dataviz
#ggtree #rstats #phylogenetics #dataviz
The trees, or pictures thereof?
ggtree, like all of Guangchang Yu’s work, is amazing for that
guangchuangyu.github.io/software/ggt...
ggtree, like all of Guangchang Yu’s work, is amazing for that
guangchuangyu.github.io/software/ggt...
ggtree
Visualization and annotation of phylogenetic trees.
guangchuangyu.github.io
December 22, 2024 at 5:17 PM
The trees, or pictures thereof?
ggtree, like all of Guangchang Yu’s work, is amazing for that
guangchuangyu.github.io/software/ggt...
ggtree, like all of Guangchang Yu’s work, is amazing for that
guangchuangyu.github.io/software/ggt...
I'm not sure what the capital I here is exactly, but it might help to use this:
ggtree(g2) + geom_tippoint(aes(color=I(color)))
more detail here: github.com/YuLab-SMU/gg...
ggtree(g2) + geom_tippoint(aes(color=I(color)))
more detail here: github.com/YuLab-SMU/gg...
feature request: phylo4d compatibility · Issue #47 · YuLab-SMU/ggtree
Hi there, Really liking ggtree - thanks so much for a great tool. One question - have you considered supporting phylo4d objects? Seems like it would be a natural fit for ggtree. As it stands, I see...
github.com
January 23, 2025 at 9:43 PM
I'm not sure what the capital I here is exactly, but it might help to use this:
ggtree(g2) + geom_tippoint(aes(color=I(color)))
more detail here: github.com/YuLab-SMU/gg...
ggtree(g2) + geom_tippoint(aes(color=I(color)))
more detail here: github.com/YuLab-SMU/gg...
I think that TreeLine also does this (as an alternative to ggtree).
January 23, 2025 at 7:45 PM
I think that TreeLine also does this (as an alternative to ggtree).
