Publications by R on Guangchuang Yu
ggtree supports phylip tree format
Phylip is also a widely used tree format, which contains taxa sequences with Newick tree text. In ggtree, we can use read.phylip() function to parse the file and use ggtree() to visualize the tree. library(ggtree) phyfile <- system.file("extdata", "sample.phy", package="ggtree") phylip <- read.phylip(phyfile) phylip ## 'phylip' S4 object that st...
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ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization
My R/Bioconductor package, ReactomePA, published in Molecular BioSystems. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization G Yu, QY He. Molecular BioSystems 2016, 12:477-479 Received: 05 Oct 2015 Accepted: 20 Nov 2015 Online: 23 Nov 2015 DOI: 10.1039/C5MB00663E Reactome is a manually curated pathway annotation...
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tweets of ggtree
Treespace visualization of a heuristic best tree search in #R package #ggtree #phylogenetics pic.twitter.com/hnSJpIABql— Alex Damián (@antropoteuthis) January 29, 2016 @guangchuangyu Updated to latest #ggtree and #ggplot2 and very impressed! Any ideas on using geom_label with tip labels to add box/fill?— Jo Williams-Newkirk (@ajwnewkirk) Jan...
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covplot supports GRangesList
To answer the issue, I extend the covplot function to support viewing coverage of a list of GRanges objects or bed files. library(ChIPseeker) files <- getSampleFiles() peak=GenomicRanges::GRangesList(CBX6=readPeakFile(files[[4]]), CBX7=readPeakFile(files[[5]])) p <- covplot(peak) print(p) By default, The coverage...
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Font Awesome supported in emojifont
emojifont is available in CRAN, you can use the following command to install it. install.packages("emojifont") An example of using emoji font in R plot is showed below: More example can be found in the post and online vignette. I found FontAwesome is quite interesting especially in technical world. In emojifont (version >= 0.3), I have packed t...
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embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function
I extended the subview function to support embed image file in a ggplot object. set.seed(123) d = data.frame(x=rnorm(10), y=rnorm(10)) imgfile <- tempfile(, fileext=".png") download.file("https://avatars1.githubusercontent.com/u/626539?v=3&u=e731426406dd3f45a73d96dd604bc45ae2e7c36f&s=140", destfile=imgfile, mode='wb') p = ggplot(d...
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KEGG Module Enrichment Analysis
KEGG MODULE is a collection of manually defined functional units, called KEGG modules and identified by the M numbers, used for annotation and biological interpretation of sequenced genomes. There are four types of KEGG modules: pathway modules – representing tight functional units in KEGG metabolic pathway maps, such as M00002 (Glycolysis, co...
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convert biological ID with KEGG API using clusterProfiler
bitr_kegg clusterProfiler can convert biological IDs using OrgDb object via the bitr function. Now I implemented another function, bitr_kegg for converting IDs through KEGG API. library(clusterProfiler) data(gcSample) hg <- gcSample[[1]] head(hg) ## [1] "4597" "7111" "5266" "2175" "755" "23046" eg2np <- bitr_kegg(hg, fromType='kegg', toTy...
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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. ChIPseeker clusterProfiler DOSE ggtree GOSemSim ReactomePA ChIPseeker Although ChIPseeker was designed for ChIP-seq annotation, I am very glad to find that someone else use it to annotate other data...
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Importing CSV data using T-SQL and R
Several ways exists to import CSV (excel) data into your SQL Server Database. One is of course, using SSIS. The other one – similar to SSIS – is using import/export function in SSMS. With wizard, you will be able to import data. Futher on, BULK INSERT (BCP) statement is to all DBA and developers very close way of importing data. Another T-SQ...
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