Publications by R on Guangchuang Yu
Phylomoji with ggtree and emojifont
With ggtree (Yu et al. 2017), it is very easy to create phylomoji. Emoji is internally supported by ggtree. Use emoji in taxa labels library(ggtree) tree_text <- "(((((cow, (whale, dolphin)), (pig2, boar)), camel), fish), seedling);" x <- read.tree(text=tree_text) ggtree(x, linetype="dashed", color='firebrick') + xlim(NA, 7) + ylim(NA, 8.5) +...
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Phylomoji with ggtree and emojifont
With ggtree (Yu et al. 2017), it is very easy to create phylomoji. Emoji is internally supported by ggtree. Use emoji in taxa labels library(ggtree) tree_text <- "(((((cow, (whale, dolphin)), (pig2, boar)), camel), fish), seedling);" x <- read.tree(text=tree_text) ggtree(x, linetype="dashed", color='firebrick') + xlim(NA, 7) + ylim(NA, 8.5) +...
1152 sym R (1273 sym/6 pcs) 12 img
[Bioc 3.5] NEWS of my BioC packages
I have 8 packages published within the Bioconductor project. ChIPseeker clusterProfiler DOSE ggtree GOSemSim meshes ReactomePA treeio A new package treeio was included in BioC 3.5 release. ChIPseeker Bug fixed of intron rank and optimized getGeneAnno function. clusterProfiler Defined simplify generics as it was removed from IRanges. enrichGO n...
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pixel art of ggplot2 faceting using geofacet
I just discovered an interesting ggplot2 extension, geofacet, that supports arranging facet panels that mimics geographic topoloty. After playing with it, I realized that it is not only for visualizing geo-related data, but also can be fun for presenting data to mimics pixel art. Here is an example using the Turkey shape: Turkey <- read.csv("htt...
731 sym R (621 sym/2 pcs) 6 img
joyplot for GSEA result
I am very glad to find that someone figure out how to use ggjoy with ggtree. I really love ggjoy and believe it can be a good tool to visualize gene set enrichment (GSEA) result. DOSE/clusterProfiler support several visualization methods. running score: enrichment map: category-gene-network: dotplot: These visualization methods are designed...
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Create memes in R
I developed a tiny toy package, meme, which is now on CRAN. As it’s name indicated, it was designed to create memes, which are captioned photos that are intended to be funny, riduculous. meme() The package is quite simple. You can use meme() function to add meme captions, and this is all the package supposed to do: library(meme) ...
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shadow text effect in grid and ggplot2 graphics
After the release of meme package, I received several feedbacks from users. The most usefule one is the comment on my blog post: Greetings Mr. Yu, I am very happy that this package exists. Thank you for making it! I would like to request a feature, to ensure the package is able to compete with professional meme-creation tools lik...
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visualizing reassortment history using seqcombo
Reassortment is an important strategy for influenza A viruses to introduce a HA subtype that is new to human populations, which creates the possibilities of pandemic. A diagram showed above (Figure 2 of doi:10.1038/srep25549) is widely used to illustrate the reassortment events. While such diagrams are mostly manually draw and edit without softw...
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Annotating phylogenetic tree with images using ggtree and ggimage
With ggimage, we are able to plot images using grammar of graphics. The layers defined in ggimage can be directly applied to ggtree to annotate phylogenetic tree using local/online image files. ggtree seamlessly work with ggimage. The geom_tiplab and geom_nodelab can accept parameter of geom="image" to parse taxa labels as image files and use the...
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setting ggplot2 background with ggbackground
ggimage 0.1.4 is available on CRAN. This release introduces a new function called ggbackground for setting image background as ggplot canvas. require(ggplot2) p <- ggplot(iris) + aes(x = Sepal.Length, y = Sepal.Width, color=Species) + geom_point(size=5) + theme_classic() Suppose we have the above ggplot object, p, the only thing we need to d...
1153 sym R (765 sym/4 pcs) 6 img