Articles by R on Guangchuang Yu

[BioC 3.2] NEWS of my BioC packages

October 15, 2015 | R on Guangchuang Yu

In BioC 3.2 release, all my packages including GOSemSim, clusterProfiler, DOSE, ReactomePA, and ChIPseeker switch from Sweave to R Markdown for package vignettes. GOSemSim To make it consistent between GOSemSim and clusterProfiler, 'worm' was deprecated and instead we should use 'celegans'. As usual, information content data was updated. Read More: 2984 Words ... [Read more...]

ChIPseq data mining with ChIPseeker

October 1, 2015 | R on Guangchuang Yu

ChIP-seq is rapidly becoming a common technique and there are a large number of dataset available in the public domain. Results from individual experiments provide a limited understanding of chromatin interactions, as there is many factors cooperate to regulate transcription. Unlike other tools that designed for single dataset, ChIPseeker is ...
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subsetting data in ggtree

September 23, 2015 | R on Guangchuang Yu

Subsetting is commonly used in ggtree as we would like to for example separating internal nodes from tips. We may also want to display annotation to specific node(s)/tip(s). Some software may stored clade information (e.g. bootstrap value) as internal node labels. Indeed we want to manipulate ...
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comic phylogenetic tree with ggtree and comicR

September 7, 2015 | R on Guangchuang Yu

ggtree applies the concepts of grammar of graphic in phylogenetic tree presentation and make it easy to add multiple layers of text and even figures above a 🌲. Here, I cartoonize a phylogenetic tree generated by ggtree with comicR, which is a funny package to generate comic (xkcd-like) graph in R. ... [Read more...]

subview

August 30, 2015 | R on Guangchuang Yu

I implemented a function, subview, in ggtree that make it easy to embed a subplot in ggplot. An example is shown below:
library(ggplot2)
library(ggtree)

dd <- data.frame(x=LETTERS[1:3], y=1:3)
pie <- ggplot(dd, aes(x=1, y, fill=x)) + 
             geom_bar(stat="identity", width=1) + 
                    coord_polar(theta="y") + theme_tree() + 
                          xlab(NULL) + ylab(NULL) + 
                               theme_transparent()

x <- sample(2:9)
y <- sample(2:9)
width <- sample(seq(0.05, 0.15, length.out=length(x)))
height <- width

p <- ggplot(data=data.frame(x=c(0, 10), y=c(0, 10)), aes(x, y))+geom_blank()
print(p)
for (i in seq_along(x)) {
    p %<>% subview(pie, x[i], y[i], width[i], height[i])
    print(p)
}
With this function, we can plot a specific clade and add a subplot of the whole topology; we can also add relative statistic graph above the tree ... [Read more...]

functional enrichment analysis with NGS data

August 20, 2015 | R on Guangchuang Yu

I found that there is a Bioconductor package, seq2pathway, that can apply functional analysis to NGS data. It consists of two components, seq2gene and gene2pathway. seq2gene converts genomic coordination to genes while gene2pathway performs functional analysis at gene level. Read More: 1007 Words Totally
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functional enrichment for GTEx paper

August 12, 2015 | R on Guangchuang Yu

The ENCODE consortium has recently published a great paper on Gene Expression from the GTEx dataset. A criticism raised on pubpeer is that the gene ontology enrichment analysis was done with DAVID which has not been updated in the last five years. The result is shown below: Read More: 1771 Words ...
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parsing BED coordinates

August 6, 2015 | R on Guangchuang Yu

In supplemental file of ChIPseeker paper. I compare distances to TSS reported by several ChIP annotation software, including ChIPseeker, ChIPpeakAnno, HOMER and PeakAnalyzer. Although I found that the chromStart positions in HOMER output have a +1 shift compare to other software, I did not realize this issue since all other software ...
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ggtree annotate phylogenetic tree with local images

July 31, 2015 | R on Guangchuang Yu

In ggtree, we provide a function annotation_image for annotating phylogenetic tree with images. To demonstrate the usage, I created a tree view from a random tree as shown below:
set.seed(2015-08-01)
p <- ggtree(rtree(10)) + xlim(0, 5)+ ylim(0, 11)
We need a data.frame that contains information of taxa labels and image paths. Here I created such a ...
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upsetplot in ChIPseeker

July 28, 2015 | R on Guangchuang Yu

ChIPseeker is an R package for ChIP peak annotation, comparison and visualization. We have implemented several visualization methods, including vennpie that was designed for viewing annotation overlap as shown below: Read More: 457 Words Totally
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ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

July 12, 2015 | R on Guangchuang Yu

My R/Bioconductor package, ChIPseeker, published in Bioinformatics. ChIPseeker had been cited by http://www.biomedcentral.com/1471-2164/16/292 and http://www.jbc.org/content/early/2015/06/18/jbc.M115.668558.short, and was used (not cited) in http://nar.oxfordjournals.org/content/early/2015/06/27/nar.gkv642.abstract and http://emboj.embopress.org/content/early/2014/12/18/...
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dotplot for enrichment result

June 22, 2015 | R on Guangchuang Yu

This is a feature request from clusterProfiler user. It's similar to what I implemented in clusterProfiler for comparing biological themes. For comparing different enrichment results, the x-axis represent different gene clusters while for a single enrichment result, the x-axis can be gene count or gene ratio. This is actually similar ...
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ggtree with funny fonts

June 12, 2015 | R on Guangchuang Yu

showtext is a neat solution to use various types of fonts in R graphs and make it easy to use funny fonts. With showtext, we can draw phylogenetic tree with different types of fonts even with symbolic/icon fonts. Read More: 638 Words Totally
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BMC favors source code plagiarism

May 27, 2015 | R on Guangchuang Yu

I found source code plagiarism a year ago and reported this case to BMC Systems Biology: I listed source code of many functions that are exactly copied from GOSemSim with only function name changed in my email. The detail of source code plagiarism can also be found at Proper use ...
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use clusterProfiler as an universal enrichment analysis tool

May 11, 2015 | R on Guangchuang Yu

clusterProfiler supports enrichment analysis of both hypergeometric test and gene set enrichment analysis. It internally support Gene Ontology analysis of about 20 species, Kyoto Encyclopedia of Genes and Genomes (KEGG) with all species that have annotation available in KEGG database, DAVID annotation, Disease Ontology and Network of Cancer Genes (via DOSE ...
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using GOSemSim to rank proteins obtained by co-IP

May 4, 2015 | R on Guangchuang Yu

Co-IP is usually used to identified interactions among specific proteins. It is widely used in detecting protein complex. Unfortunately, an identified protein may not be an interactor, and sometimes can be a background contaminant. Ranking proteins can help us to focus a study on a few high quality candidates for ...
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