Publications by R on Guangchuang Yu
[BioC 3.2] NEWS of my BioC packages
In BioC 3.2 release, all my packages including GOSemSim, clusterProfiler, DOSE, ReactomePA, and ChIPseeker switch from Sweave to R Markdown for package vignettes. GOSemSim To make it consistent between GOSemSim and clusterProfiler, ‘worm’ was deprecated and instead we should use ‘celegans’. As usual, information content data was updated....
4224 sym
use simplify to remove redundancy of enriched GO terms
To simplify enriched GO result, we can use slim version of GO and use enricher function to analyze. Another strategy is to use GOSemSim to calculate similarity of GO terms and remove those highly similar terms by keeping one representative term. To make this feature available to clusterProfiler users, I develop a simplify method to reduce redunda...
2114 sym R (213 sym/4 pcs) 6 img 2 tbl
Comparison of clusterProfiler and GSEA-P
Thanks @mevers for raising the issue to me and his efforts in benchmarking clusterProfiler. He pointed out two issues: outputs from gseGO and GSEA-P are poorly overlap. pvalues from gseGO are generally smaller and don’t show a lot of variation For GSEA analysis, we have two inputs, a ranked gene list and gene set collections. First of all, th...
5018 sym R (2813 sym/13 pcs) 6 img 6 tbl
phylomoji with ggtree
If you search the hashtag, #phylomoji, in twitter, you can find many creative phylogenetic tree constructed with emoji. #phylomoji with Darwin's water bears! @OxyEvo | | |_____| | |_____| |_____| | — Matthew Weiser (@weisguy318) September 16, 2015 #Phylomoji MicroRNAs ” class=”wp-smiley” style=...
2829 sym R (111 sym/2 pcs) 28 img 1 tbl
R kernel in Jupyter notebook 3
I followed the post, Installing an R kernel for IPython/jupyter notebook 3 on OSX, to install jupyter with python3 and R kernels in my iMac. I have elementaryOS on my Macbook Pro and also want to have jupyter on it. The installation process is quite similar. Install Jupyter ?View Code BASH1 2 sudo apt-get install python3-pip sudo pip3 install jup...
1416 sym R (353 sym/8 pcs) 2 img 4 tbl
use emoji font in R
I have played with emoji in R for a while. My solution of using it is different from what implemented in emoGG. emoGG is a good attemp to add emoji in ggplot2. It render emoji picture (png) and creat a layer, geom_emoji, to add emoji. In my opinion, emoji should be treated as ordinary font in user interface, albeit it maynot be true internally. I...
1618 sym R (1869 sym/7 pcs) 12 img
News of ggtree
A new version of ggtree that works with ggplot2 (version >= 2.0.0) is now availabel. new layers Some functions, add_legend, hilight, annotation_clade and annotation_clade2 were removed. Instead we provide layer functions, geom_treescale, geom_hilight and geom_cladelabel. You can use + operator to add layers using these layer functions. In addtion...
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GO analysis using clusterProfiler
clusterProfiler supports over-representation test and gene set enrichment analysis of Gene Ontology. It supports GO annotation from OrgDb object, GMT file and user’s own data. support many species In github version of clusterProfiler, enrichGO and gseGO functions removed the parameter organism and add another parameter OrgDb, so that any specie...
2436 sym R (26834 sym/10 pcs) 10 img
Annotate a phylogenetic tree with insets
ggtree implemented a function, subview, that can add subplots on a ggplot2 object. It had successful applied to plot pie graphs on map. set.seed(2016-01-04) tr <- rtree(30) tr <- groupClade(tr, node=45) p <- ggtree(tr, aes(color=group)) + geom_tippoint() cpos <- get_clade_position(p, node=45) p1 <- p + geom_hilight(node=45) p2 <- with(cpos, p+xli...
1920 sym R (1641 sym/9 pcs) 18 img
label edge number in ggtree
This is a question from ggtree user. In ape and phytools, it’s easy to label edge using the edgelabels function. set.seed(1) tr = rtree(30) library(ape) plot(tr, main="ape") edgelabels() I don’t see any necessity to label edge numbers, as they are meaningless. The number is labeled as the row index of tr$edge, and edge can be uniquely mapped...
927 sym R (308 sym/2 pcs) 4 img