r plot, phangorn package

In R in Ubuntu 12.04,

when you install and use the "phangorn" package, you might get such error:

install.packages("phangorn")
library(phangorn)

configure: error: missing required header GL/gl.h
ERROR: configuration failed for package ‘rgl’

normally means you haven't installed the -dev version of a package, in this case GL, and you will need to install: 

sudo apt-get install mesa-common-dev
sudo apt-get install libglu1-mesa-dev 
sudo apt-get install freeglut3-dev 
sudo apt-get install mesa-common-dev

You might get the following error later (in R) because of a tcl b**/gripe/compliant: Error in structure(.External(.C_dotTcl, ...), class = "tclObj") : [tcl] can't find package BWidget.

To fix this problem, if you have it:

install at the regular terminal:

sudo apt-get install bwidget




R plot, tricky input of cex

In R plot,

For example:

plot(...... pch=20, cex=0.5)

Here, the 'cex' controls the size of the symbol. But if this value is passed in from another variable or from command line, it has to be converted to integer or numeric value (the numeric value is better).

For example:

my.cex.size = as.numeric(args[1])

plot(...... pch=20, cex=my.cex.size)

MAC OS 中的 virtualbox 安装Win7

准备工作:
把64位win7系统安装盘用软件转换成iso格式

下载mac版本virtualbox
在virtualbox中选择64位系统
选择usb中的iso文件

保留基本设置
安装系统

显示问题

网络问题

RefSeq prefix explaination

Accession prefix	Molecule type	Comment
AC_	Genomic	Complete genomic molecule, usually alternate assembly
NC_	Genomic	Complete genomic molecule, usually reference assembly
NG_	Genomic	Incomplete genomic region
NT_	Genomic	Contig or scaffold, clone-based or WGSa
NW_	Genomic	Contig or scaffold, primarily WGSa
NS_	Genomic	Environmental sequence
NZ_b	Genomic	Unfinished WGS
NM_	mRNA
NR_	RNA
XM_c	mRNA	Predicted model
XR_c	RNA	Predicted model
AP_	Protein	Annotated on AC_ alternate assembly
NP_	Protein	Associated with an NM_ or NC_ accession
YP_c	Protein
XP_c	Protein	Predicted model, associated with an XM_ accession
ZP_c	Protein	Predicted model, annotated on NZ_ genomic records

Detailed link here: http://www.ncbi.nlm.nih.gov/books/NBK21091/