Blog Archives

embeding a subplot in ggplot via subview

August 30, 2015
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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: Read More: 131 Words Totally

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functional enrichment analysis with NGS data

August 20, 2015
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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. Read More: 1007 Words Totally

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functional enrichment for GTEx paper

August 12, 2015
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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: Read More: 1771 Words Totally

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parsing BED coordinates

August 6, 2015
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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 consistent. Read More: 1102 Words...

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[ggtree] annotate phylogenetic tree with local images

August 1, 2015
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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: Read More: 973 Words Totally

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upsetplot in ChIPseeker

July 28, 2015
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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: Read More: 457 Words Totally

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[paper published] ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

July 13, 2015
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[paper published] ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

My R/Bioconductor package, ChIPseeker, published in Bioinformatics. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization Read More: 992 Words Totally

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flip and rotate branches in ggtree

June 30, 2015
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flip and rotate branches in ggtree

flip function is a feature request from ggtree user. It accepts a tree view and two node numbers and exchange the positions of the selected clades. ?View Code RSPLUS1 Read More: 159 Words Totally

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dotplot for enrichment result

June 22, 2015
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dotplot for enrichment result

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 to traditional barplot, with dot position as bar height...

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ggtree with funny fonts

June 12, 2015
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ggtree with funny fonts

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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