flip and rotate branches in ggtree

flip function is a feature request from ggtree user. It accepts a tree view and two node numbers and exchange the positions of the selected clades.

?View Code RSPLUS
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require(ggtree)
set.seed(2015-07-01)
tr < - rtree(30)
p <- ggtree(tr) + geom_text(aes(label=node))
gridExtra::grid.arrange(p, flip(p, 38, 33), ncol=2)

It's chainable and all possible position adjustment can be achieved via multiple flip operations.
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dotplot for enrichment result

This is a feature request from clusterProfiler user. It's similar to what I implemented in clusterProfiler for comparing biological themes. For comparing different enrichment results, the x-axis represent different gene clusters while for a single enrichment result, the x-axis can be gene count or gene ratio. This is actually similar to traditional barplot, with dot position as bar height and dot color as bar color. But dotplot can represent one more feature nicely by dot size and it can be a good alternative to barplot.

?View Code RSPLUS
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library(DOSE)
deg = names(geneList)[abs(geneList) > 1]
do = enrichDO(deg)
dotplot(do, showCategory=20)


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ggtree with funny fonts

showtext is a neat solution to use various types of fonts in R graphs and make it easy to use funny fonts.

With showtext, we can draw phylogenetic tree with different types of fonts even with symbolic/icon fonts.

?View Code RSPLUS
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require(showtext)
 
font.add.google("Gochi Hand", "gochi")
font.add.google("Rock Salt", "rock")
 
link = "http://img.dafont.com/dl/?f=wm_people_1";
download.file(link, "wmpeople1.zip", mode = "wb");
unzip("wmpeople1.zip");
font.add("wmpeople1", "wmpeople1.TTF");
 
link = "http://img.dafont.com/dl/?f=emoticons";
download.file(link, "emoticons.zip", mode = "wb");
unzip("emoticons.zip");
font.add("emoticons", "emoticons.ttf");
 
 
showtext.auto()
set.seed(2015-05-14)
 
library(ggplot2)
library(ggtree)
 
tree < - rtree(30)
ggtree(tree, color="darkgreen") + geom_tiplab(family="gochi") + theme_classic() +
    theme(axis.text.x=element_text(size=rel(4), family="emoticons", color="firebrick")) +
        scale_y_continuous(breaks=seq(0, 30, 4), labels=letters[c(12:17, 20, 21)]) +
            theme(axis.text.y=element_text(size=rel(4), family="wmpeople1", color="#FDAC4F")) +
                annotate("text", x=2, y=18, label="Have fun with ggtree!",
                         family="rock", angle=30, size=12, color="steelblue")

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BMC包庇代码抄袭

ppiPre抄袭了GOSemSim的代码,证据当然非常充分,比对一下代码就知道了,我在Proper use of GOSemSim一文中,做出了一些比较,另外也可以参考github页面,github记录了ppiPre被暴光抄袭之后所做的修改。

从我给BMC Systems Biology的编辑反馈这件事开始,在这铁板钉钉的事实面前,编辑拖了整整一年,而这一年时间过去了,ppiPre仍没有被编辑部受理。从最早反应这件事情,编辑信誓旦旦说他们很重视这种事情,到后面对我的邮件视而不见,我愿意相信编辑部处理这些事情,需要时间,他们有自己的规则,但一年的时间,不回邮件,冷处理以淡化此事,这绝对不是应该有的规则。

在编辑一直无视我的情况下,我写出了Proper use of GOSemSim一文,列举了一些一模一样的代码,并告知CRAN,当ppiPre被CRAN移除时,我写信给编辑,这时候,编辑告诉我说他们准备要去联系作者了,这时候已经过去半年了,是的!你没有看错,半年过去了,编辑说他们还没去联系作者!我是不相信的。必然是联系了之后,有某些不为人知的原因,所以编辑态度反常,对抄袭这种打鸡血的事情,不断在打太极。

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BMC favors source code plagiarism

I found source code plagiarism a year ago and reported this case to BMC Systems Biology:

I listed source code of many functions that are exactly copied from GOSemSim with only function name changed in my email. The detail of source code plagiarism can also be found at Proper use of GOSemSim.

I got reply from the Editor 3 days after (see screenshot).
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