violin plot

ggplot2 0.9.0版本将在3月1号发布,改动较大,最近bioc mailing list也有诸多讨论,因为它导致了某些包编译出错(估计是NAMESPACE引起的)。

按照hadley的说法是这是为了把他个人的项目变成一个社区项目。

大多数的改动对用户来说是invisible的,用roxygen2去注释函数,核心代码使用S3重写,分离出一些特性(scales包)等。

最明显的是现在画图速度变快了,不过我觉得最让人兴奋的是guide_legend()guide_colorbar()两个函数,可以修改legend.

画图的话,加了四个函数geom_map(), geom_raster(),geom_dotplot()geom_violin().
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今天在微博上看到这坑爹的方程: $ (x^2+y^2-1)^3 = {x^2} {y^3}$ 画出来如下: 跟个屁股似的,sigh… 翻出azalea的老文:http://azaleasays.com/2008/06/18/fomula-of-love/ 用ggplot2画一下这个爱的方程:$17x^2-16|x|y+17y^2 = 225 $ x <- seq(-sqrt(17), sqrt(17), 0.001) y1 <- 8abs(x)/17 + 15 sqrt(17 - x^2)/17 y2 <- 8abs(x)/17 - 15 sqrt(17 - x^2)/17 d <- data.frame(x=c(x,x),y=c(y1,y2)) require(ggplot2) p <- ggplot(d, aes(x,y)) p + geom_point(color="red") 还可以画出红心,适合今天七夕的日子。 p + geom_line(color="red") 画函数图,这种事情,还是用CAS方便点。 通过maxima来画,一条指令就行,还不用解方程: contour_plot(17*x^2-16*abs(x)*y+17*y^2-225, [x,-sqrt(17),sqrt(17)],[y,-15*sqrt(17)/17, sqrt(17)])
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screen shot

买了苹果机,一直放在家里没用,准备开会带去用,拿过来装几个软件。

校园网用锐捷是个比较讨厌的东西。当年在华农,光这认证就搞了很久。

现在开源的认证客户端多了,搞起来也方便了,现在在linux下用的xmuruijie,就比当年mystar好用。

估计xmuruijie也是可以在苹果机上用的,依赖python,搞不好还有些modules要装,懒得去弄,搜了一下,找到mentohust,当然需要改一下mac address,用万能的ifconfig搞定。

为了编译软件,必要先装xcode,这个大家伙,4G多,中午挂到吃晚饭才下完。 然后就可以装各种open source的软件。

mac上有fink支持debian一样的apt-get,还有原生的macport,gentoo的portage也支持,我选择使用netbsd的pkgsrc来安装各种开源软件。

以前用过比较长时间的netbsd,用着比较顺手。


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Ewan Birney最近的一篇博文(Five statistical things I wished I had been taught 20 years ago )讲述了统计对于生物学的重要性。

一开始从RA Fisher讲起,说生物压根就是统计。Fisher是个农业学家,他所建立的那些统计方法,都是从生物学问题出发。

Ewan所谈及的五个方面分别是:

1. Non parametric statistics. These are statistical tests which make a bare minimum of assumptions of underlying distributions; in biology we are rarely confident that we know the underlying distribution, and hand waving about central limit theorem can only get you so far. Wherever possible you should use a non parameteric test. This is Mann-Whitney (or Wilcoxon if you prefer) for testing “medians” (Medians is in quotes because this is not quite true. They test something which is closely related to the median) of two distributions, Spearman’s Rho (rather pearson’s r2) for correlation, and the Kruskal test rather than ANOVAs (though if I get this right, you can’t in Kruskal do the more sophisticated nested models you can do with ANOVA). Finally, don’t forget the rather wonderful Kolmogorov-Smirnov (I always think it sounds like really good vodka) test of whether two sets of observations come from the same distribution. All of these methods have a basic theme of doing things on the rank of items in a distribution, not the actual level. So - if in doubt, do things on the rank of metric, rather than the metric itself.


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As an in vitro model for type II human lung cancer, A549 cells resist cytotoxicity via phosphorylation of proteins as demonstrated by many studies. However, to date, no large-scale phosphoproteome investigation has been conducted on A549. Here, we performed a systematical analysis of the phosphoproteome of A549 by using mass spectrometry (MS)-based strategies. This investigation led to the identification of 337 phosphorylation sites on 181 phosphoproteins. Among them, 67 phosphoproteins and 230 phosphorylation sites identified appeared to be novel with no previous characterization in lung cancer.
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机房放着台机架机,闲着也是耗电,平时偶尔用putty登上去,没有图形界面还是有些不方便。

搜了一下,发现好几个软件可做这样的事,Xming是开源的,所以选择使用Xming+putty来远程连linux的桌面。

试用了一下,果然不错。

需要修改/etc/ssh/sshd_config,添加:

X11Forwrding yes

需要配置一下PuTTY,Connection-SSh-X11中选中Enable X11forwarding 其中X display location里填入localhost:0

运行Xming,再用putty连到服务器上,运行程序,就OK了。就好像windows下的本地程序一般。整合性很好。


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Author's picture

Guangchuang Yu

a senior-in-age-but-not-senior-in-knowledge bioinformatician

PhD student

Hong Kong