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[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:

using meshes for MeSH Enrichment Analysis

MeSH (Medical Subject Headings) is the NLM (U.S. National Library of Medicine) controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH is comprehensive life science vocabulary. MeSH has 19 categories and MeSH.db contains 16 of them. That is:

leading edge analysis

leading edge and core enrichment

Leading edge analysis reports Tags to indicate the percentage of genes contributing to the enrichment score, List to indicate where in the list the enrichment score is attained and Signal for enrichment signal strength.

It would also be very interesting to get the core enriched genes that contribute to the enrichment.

Now DOSE, clusterProfiler and ReactomePA all support leading edge analysis and report core enriched genes.

How to bug author

As an author of several Bioconductor packages. I found many questions from users are quite annoying. Some of them never use google and they are reluctant to read vignettes.

Step 1: make sure you are using the latest release

I found many peoples are using out-of-date packages. When they got an issue of an out-dated package, they never check whether the issue still exists in latest release.

identify method for ggtree

We are happy to announce that ggtree supports interactive tree annotation/manipulation by implementing an identify method. Users can click on a node to highlight a clade, to label or rotate it etc.

Here is an example of highlighting clades using geom_hilight with identify:

[Bioc 33] NEWS of my BioC packages

Today is my birthday and it happened to be the release day of Bioconductor 3.3. It’s again the time to reflect what I’ve done in the past year.