Articles by R on Guangchuang Yu

rename phylogeny tip labels in treeio

April 18, 2018 | R on Guangchuang Yu

I don’t know whether ‘rename taxa’ is a common task or not. It seems not a good idea to rename taxa in Newick tree text, since it may introduce problems when mapping the original sequence alignment to the tree. If you just want to show different or additional information ...

setting ggplot2 background with ggbackground

April 18, 2018 | R on Guangchuang Yu

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 do is passing the p with an image file name (local or remote) to ggbackground, ...

Annotating phylogenetic tree with images using ggtree and ggimage

February 28, 2018 | R on Guangchuang Yu

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 ...

visualizing reassortment history using seqcombo

December 4, 2017 | R on Guangchuang Yu

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 ...

shadow text effect in grid and ggplot2 graphics

November 2, 2017 | R on Guangchuang Yu

After the release of meme package, I received several feedbacks from users. The most usefule one is the comment on my blog post: Sercan Kahveci 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 ...

Create memes in R

October 25, 2017 | R on Guangchuang Yu

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 ...

joyplot for GSEA result

August 20, 2017 | R on Guangchuang Yu

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...

pixel art of ggplot2 faceting using geofacet

June 26, 2017 | R on Guangchuang Yu

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 ...

[Bioc 3.5] NEWS of my BioC packages

May 19, 2017 | R on Guangchuang Yu

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 now supports ont="ALL" ... [Read more...]

Phylomoji with ggtree and emojifont

May 16, 2017 | R on Guangchuang Yu

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

Phylomoji with ggtree and emojifont

May 16, 2017 | R on Guangchuang Yu

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

convert graphic object to tree object using treeio

January 3, 2017 | R on Guangchuang Yu

I have splitted ggtree to 2 packages, treeio and ggtree. Now ggtree is mainly focus on visualization and annotation, while treeio focus on parsing and exporting tree files. Here is a welcome message from treeio that you can convert ggtree output to tree object which can be exported as newick or ...

convert graphic object to tree object using treeio

January 1, 2017 | R on Guangchuang Yu

I have splitted ggtree to 2 packages, treeio and ggtree. Now ggtree is mainly focus on visualization and annotation, while treeio focus on parsing and exporting tree files. Here is a welcome message from treeio that you can convert ggtree output to tree object which can be exported as newick or ...

dotplot for GSEA result

December 29, 2016 | R on Guangchuang Yu

For GSEA analysis, we are familar with the above figure which shows the running enrichment score. But for most of the software, it lack of visualization method to summarize the whole enrichment result. In DOSE (and related tools including clusterP...

dotplot for GSEA result

December 29, 2016 | R on Guangchuang Yu

For GSEA analysis, we are familar with the above figure which shows the running enrichment score. But for most of the software, it lack of visualization method to summarize the whole enrichment result. In DOSE (and related tools including clusterPro...

add layer to specific panel of facet_plot output

December 28, 2016 | R on Guangchuang Yu

This is a question from ggtree google group: Dear ggtree team, how can I apply a geom_xxx to only one facet panel? For example if i want to get geom_hline(yintersect=1:30) or a geom_text() in the dot panel? I cant see the facet_grid(. ~ var) function call, ...

add layer to specific panel of facet_plot output

December 27, 2016 | R on Guangchuang Yu

This is a question from ggtree google group: Dear ggtree team, how can I apply a geom_xxx to only one facet panel? For example if i want to get geom_hline(yintersect=1:30) or a geom_text() in the dot panel? I cant see the facet_grid(. ~ var) function call, ...

ggtree version of plotTree

December 16, 2016 | R on Guangchuang Yu

PLOTTING TREES + DATA is difficult. @DrKatHolt developed plotTree (R and Python scripts) to visualize associated data with trees, e.g. heatmap, horizontal bar etc. I reproduced the examples presented in the plotTree repo using ggtree. Source code is f...

ggtree version of plotTree

December 16, 2016 | R on Guangchuang Yu

PLOTTING TREES + DATA is difficult. @DrKatHolt developed plotTree (R and Python scripts) to visualize associated data with trees, e.g. heatmap, horizontal bar etc. I reproduced the examples presented in the plotTree repo using ggtree. Source code is...

Edge coloring with user data

December 11, 2016 | R on Guangchuang Yu

Coloring edges in ggtree is quite easy, as we can map the color to numerical or categorical values via the aes(color=VAR) syntax. For user’s own data, it is also easy as ggtree provide the %

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