Articles by R on Guangchuang Yu

rename phylogeny tip labels in treeio

April 18, 2018 | 0 Comments

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 ...
[Read more...]

Annotating phylogenetic tree with images using ggtree and ggimage

February 28, 2018 | 0 Comments

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 ...
[Read more...]

visualizing reassortment history using seqcombo

December 4, 2017 | 0 Comments

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 ...
[Read more...]

shadow text effect in grid and ggplot2 graphics

November 2, 2017 | 0 Comments

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 ...
[Read more...]

Create memes in R

October 25, 2017 | 0 Comments

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 ...
[Read more...]

joyplot for GSEA result

August 20, 2017 | 0 Comments

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...
[Read more...]

pixel art of ggplot2 faceting using geofacet

June 26, 2017 | 0 Comments

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 ...
[Read more...]

[Bioc 3.5] NEWS of my BioC packages

May 19, 2017 | 0 Comments

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...]

convert graphic object to tree object using treeio

January 3, 2017 | 0 Comments

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 ...
[Read more...]

convert graphic object to tree object using treeio

January 1, 2017 | 0 Comments

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 ...
[Read more...]

dotplot for GSEA result

December 29, 2016 | 0 Comments

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...
[Read more...]

dotplot for GSEA result

December 29, 2016 | 0 Comments

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...
[Read more...]

add layer to specific panel of facet_plot output

December 28, 2016 | 0 Comments

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, ...
[Read more...]

add layer to specific panel of facet_plot output

December 27, 2016 | 0 Comments

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, ...
[Read more...]

ggtree version of plotTree

December 16, 2016 | 0 Comments

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...
[Read more...]

ggtree version of plotTree

December 16, 2016 | 0 Comments

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...
[Read more...]

Edge coloring with user data

December 11, 2016 | 0 Comments

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 %
[Read more...]
1 2 3 8

Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)