Publications by R on Guangchuang Yu
upsetplot in ChIPseeker
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: Not all overlap information can be demonstrated in vennpie. Upset is an effective way to visualize sets and intersections. We impo...
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ggtree annotate phylogenetic tree with local images
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...
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parsing BED coordinates
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 are consisten...
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functional enrichment for GTEx paper
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: It would be interest to see if results change by using clusterProfiler t...
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functional enrichment analysis with NGS data
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. I think it would be interesting to incorporate seq2gene with clusterProf...
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subview
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() + ...
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embeding a subplot in ggplot via subview
I implemented a function, subview, in ggtree that make it easy to embed a subplot in ggplot. An example is shown below: ?View Code RSPLUS1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 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", w...
1182 sym R (679 sym/2 pcs) 6 img 1 tbl
comic phylogenetic tree with ggtree and comicR
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. Have fun with ggtree and comicR. ?View Code RSPLU...
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subsetting data in ggtree
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 such information and taxa labels separately. In curren...
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ChIPseq data mining with ChIPseeker
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 desi...
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