Blog Archives

rename phylogeny tip labels in treeio

April 18, 2018
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rename phylogeny tip labels in treeio

I don’t know whether ‘rename taxa’ is a common task or not. It seems not a good idea to rename taxa in Newick tree text, since it may introduce problems when mapping the original sequence alignment to the tree. If you just want to show different or additional information when plotting the tree, it is fine and easy to do...

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setting ggplot2 background with ggbackground

April 18, 2018
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setting ggplot2 background with ggbackground

ggimage 0.1.4 is available on CRAN. This release introduces a new function called ggbackground for setting image background as ggplot canvas. require(ggplot2) p

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Annotating phylogenetic tree with images using ggtree and ggimage

February 28, 2018
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Annotating phylogenetic tree with images using ggtree and ggimage

With ggimage, we are able to plot images using grammar of graphics. The layers defined in ggimage can be directly applied to ggtree to annotate phylogenetic tree using local/online image files. ggtree seamlessly work with ggimage. The geom_tiplab and geom_nodelab can accept parameter of geom="image" to parse taxa labels as image files and use them to “label” the taxa using...

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visualizing reassortment history using seqcombo

December 4, 2017
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visualizing reassortment history using seqcombo

Reassortment is an important strategy for influenza A viruses to introduce a HA subtype that is new to human populations, which creates the possibilities of pandemic. A diagram showed above (Figure 2 of doi:10.1038/srep25549) is widely used to illustrate the reassortment events. While such diagrams are mostly manually draw and edit without software tool to automatically generate. Here, I implemented the hybrid_plot function for producing publication...

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shadow text effect in grid and ggplot2 graphics

November 2, 2017
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shadow text effect in grid and ggplot2 graphics

After the release of meme package, I received several feedbacks from users. The most usefule one is the comment on my blog post: Sercan Kahveci Greetings Mr. Yu, I am very happy that this package exists. Thank you for making it! I would like to request a feature, to ensure the package is able to compete with professional meme-creation tools like memegenerator and...

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Create memes in R

October 25, 2017
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Create memes in R

I developed a tiny toy package, meme, which is now on CRAN. As it’s name indicated, it was designed to create memes, which are captioned photos that are intended to be funny, riduculous. meme() The package is quite simple. You can use meme() function to add meme captions, and this is all the package supposed to do: library(meme) u

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joyplot for GSEA result

August 20, 2017
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joyplot for GSEA result

I am very glad to find that someone figure out how to use ggjoy with ggtree. I really love ggjoy and believe it can be a good tool to visualize gene set enrichment (GSEA) result. DOSE/clusterProfiler support several visualization methods. running...

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pixel art of ggplot2 faceting using geofacet

June 26, 2017
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pixel art of ggplot2 faceting using geofacet

I just discovered an interesting ggplot2 extension, geofacet, that supports arranging facet panels that mimics geographic topoloty. After playing with it, I realized that it is not only for visualizing geo-related data, but also can be fun for presenting data to mimics pixel art. Here is an example using the Turkey shape: Turkey

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[Bioc 3.5] NEWS of my BioC packages

May 19, 2017
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I have 8 packages published within the Bioconductor project. ChIPseeker clusterProfiler DOSE ggtree GOSemSim meshes ReactomePA treeio A new package treeio was included in BioC 3.5 release. ChIPseeker Bug fixed of intron rank and optimized getGeneAnno function. clusterProfiler Defined simplify generics as it was removed from IRanges. enrichGO now supports ont="ALL" and will test three GO ontologies simultaneously. dotplot for compareClusterResult not supports three GO sub-ontologies. bitr_kegg supports converting Path/Module to geneID and vice versa. plotGOgraph...

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Phylomoji with ggtree and emojifont

May 16, 2017
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Phylomoji with ggtree and emojifont

With ggtree (Yu et al. 2017), it is very easy to create phylomoji. Emoji is internally supported by ggtree. Use emoji in taxa labels library(ggtree) tree_text

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