# Recent Publications

More Publications

• ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

• ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization

• ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

• DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis

• Putative cobalt- and nickel-binding proteins and motifs in Streptococcus pneumoniae

• A novel andrographolide derivative AL-1 exerts its cytotoxicity on K562 cells through a ROS-dependent mechanism

• LXtoo: an integrated live Linux distribution for the bioinformatics community

• clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

• Functional similarity analysis of human virus-encoded miRNAs

• A new method for measuring functional similarity of microRNAs

# Posts

### [Bioc 34] NEWS of my BioC packages

I have 7 packages published within the Bioconductor project.

A new package meshes was included in BioC 3.4 release.

### reproducible logo generated by ggtree

ggtree provides many helper functions for manupulating phylogenetic trees and make it easy to explore tree structure visually.

Here, as examples, I used ggtree to draw capital character G and C, which are first letter of my name :-).

To draw a tree in such shape, we need fan layout (circular layout with open angle) and then rotating the tree to let the open space on the correct position. Here are the source codes to produce the G and C shapes of tree. I am thinking about using the G shaped tree as ggtree logo. Have fun with ggtree :-)

### ggtree for outbreak data

OutbreakTools implements basic tools for the analysis of Disease Outbreaks.

It defines S4 class obkData to store case-base outbreak data. It also provides a function, plotggphy, to visualize such data on the phylogenetic tree.

library(OutbreakTools)
data(FluH1N1pdm2009)
attach(FluH1N1pdm2009)

x <- new("obkData", individuals = individuals, dna = FluH1N1pdm2009$dna, dna.individualID = samples$individualID, dna.date = samples$date, trees = FluH1N1pdm2009$trees)

plotggphy(x, ladderize = TRUE, branch.unit = "year",
tip.color = "location", tip.size = 3, tip.alpha = 0.75)


### ggtree for microbiome data

ggtree can parse many software outputs and the evolution evidences inferred by these software can be used directly for tree annotation. ggtree not only works as an infrastructure that enables evolutionary data that inferred by commonly used software packages to be used in R, but also serves as a general tree visualization and annotation tool for the R community as it supports many S3/S4 objects defined by other R packages.

## phyloseq for microbiome data

phyloseq class defined in the phyloseq package was designed for microbiome data. phyloseq package implemented plot_tree function using ggplot2. Although the function was implemented by ggplot2 and we can use theme, scale_color_manual etc for customization, the most valuable part of ggplot2, adding layer, is missing. plot_tree only provides limited parameters to control the output graph and it is hard to add layer unless user has expertise in both phyloseq and ggplot2.

### ggtree paper published

Today ggtree received 100 stars on and I found the paper was online at the same day by the tweet:

# Teaching

I am a teaching instructor for the following courses at University X: