GitHub Notes to ... myself

Downloading github repo into a local folder

git clone https://github.com/vladpetyuk/MSnID.git

Assuming I am using RStudio, start a new project from existing directory. In this example that would be MSnID.

How to update your fork, so it catches up with original?
It is discussed here Basically issue a pull request where is the base is your own repository and head is the original that your forked from. Note that the default is the opposite: base - the original, head - you. You have to switch it using the drop-down menu.

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An example of handling gist from GitHub

• create directory where the gists are going to be stored
• git clone https://gist.github.com/8607045.git
• the new directory 8607045 will be created
• cd 8607045
• git add .
• edit the file
• to check what is going on: git status
• git commit -m "your commit message"
• git push

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Pushing local repo to GitHub
Described here. Basically in my case, when git already exists. I need to

Create a new repository on GitHub. Do not initialize the new repository with anything yet! (in example below - simulant.LCMS)

git remote add origin https://github.com/vladpetyuk/simulant.LCMS.git

git remote -v

git push -u origin master

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Greyed out push and pull in Rstudio
fix explained here

Mimicking Object-Oriented Behavior with R Functions (that is Closures)

Actually, there is already a number of ways and packages object-oriented semantics implemented in R. It is nicely summarize in the Table 1 of this article. Let's assume for a moment this diversity of object-oriented approaches in R is not enough. There is an unbearable urge to implement yet another one. Well... let's exploit the fact that functions in R are not functions in a C++ or even Python sense. They are closures. Put in a simple terms it is a function that packaged up with some state. That state (environment in case of R) may contain variables and functions. A couple of other posts on a somewhat relevant topic that I may suggest are here and here.

Updating values in hierarchical lists

How to parse and update a hierarchical list using an elegant single command? A lot of things can be done with a single command in R. This (after a few considerations) turned out not an exception either.

Fixing the blurry R fonts caused by DPI scaling on Windows 7

R does not play well with high DPI scaling on Windows 7.  Fonts look blurry on my 27 inch WHDQ monitor with 150% DPI scaling.  Fixing that for 32-bit R was easy.  Go to the properties of C:\Program Files\R\R-3.0.2\bin\i386\Rgui.exe. Note, you may need to replace the R version number in that path. Then open the "Compatibility" tab check the box "Disable display scaling on high DPI settings" and you are done. Once you try to do the same for 64-bit counterpart C:\Program Files\R\R-3.0.2\bin\x64\Rgui.exe you'll see the grayed out check box that can not be altered. The solutions requires editing the registry and is described here
http://superuser.com/questions/355915/vista-dpi-scaling-cannot-disable-dpi-scaling-for-wireshark/355953#355953?s=97656833-4e08-4a55-8773-1fe68b5fca77
Brief instructons.

Go to
HKEY_CURRENT_USER\Software\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers
Most likely you'll already see a setting for 32-bit Rgui.exe
Make a similar one by right clicking on the "Layer" and add new string value.
Name: C:\Program Files\R\R-3.0.2\bin\x64\Rgui.exe
Type: REG_SZ
Data: HIGHDPIAWARE

Formatting code on blogger

http://stackoverflow.com/questions/679189/formatting-code-snippets-for-blogging-on-blogger



This one is using gist

Collection of resources explaining Bioconductor facilities

http://www.mas.ncl.ac.uk/~ncsg3/microarray/

Exploring S4 Objects in R

Looking what is inside of a particular method.
Method - spectra
Class - MSnExp
If method is exported (check NAMESPACE) then this will work.

getMethod("spectra","MSnExp")

Method Definition:
function (object) 
{
    sl <- as.list(assayData(object))
    fnames <- featureNames(object)
    return(sl[fnames])
}

Signatures:
        object  
target  "MSnExp"
defined "MSnExp"

Showing slots for a given class

showClass("MSnExp")

showMethods(classes="MSnExp", where="package:MSnbase")

The link to check http://missingreadme.wordpress.com/2011/01/04/how-to-see-the-code-for-s4-methods-in-r/

Debugging
trace(show, tracer=browser, signature=c(x="eSet"), where=getNamespace("Biobase"))

Where are the R libraries?

on Mac
/Library/Frameworks/R.framework/Versions/3.0/Resources/library
on Win
c:/Users/vlad/R/win-library/3.0

Passing-by-reference in R

collection of links to debates/tricks on passing-by-reference in R. http://stackoverflow.com/questions/2603184/r-pass-by-reference
http://www.stat.berkeley.edu/~paciorek/computingTips/Pointers_passing_reference_.html
https://stat.ethz.ch/pipermail/r-devel/2009-January/051899.html
http://homepage.stat.uiowa.edu/~luke/R/references.html
http://r.789695.n4.nabble.com/Pass-By-Value-Questions-td2331565.html

My take on that is to use new Reference Classes if there is a need for complex mutable objects.
Use of environments to pass-by-reference is considered as a hack.
E.g. (from Robert Gentleman's book)
e1 = new.env()
f = function(x) {x+z}
enironment(f) = e1
e1$z = 10
f(1)
Output is 11
Note, however, after deleting e1, f does not go away.
rm(e1)
f is still around

Second point is to take a look at data.frame by pass-by-reference using "ref" and "plyr" packages.

customizing R

On windows:
C:\Program Files\R\R-2.15.1\etc\Rprofile.site

My Rprofile with added custom color schemes

# Things you might want to change

# options(papersize="a4")

# options(editor="notepad")

# options(pager="internal")

# set the default help type

# options(help_type="text")

  options(help_type="html")

# set a site library

# .Library.site <- file.path(chartr("\\", "/", R.home()), "site-library")

# set a CRAN mirror

# local({r <- getOption("repos")

#       r["CRAN"] <- "http://my.local.cran"

#       options(repos=r)})

# Give a fortune cookie, but only to interactive sessions

# (This would need the fortunes package to be installed.)

if (interactive()) {

   fortunes::fortune()

   

   #---- custom color schemes

   library(grDevices)

   blue.colors = colorRampPalette(RColorBrewer::brewer.pal(9,"Blues"))

   jet.colors = colorRampPalette(c("blue","#007FFF","cyan","#7FFF7F","yellow","#FF7F00","red"))

   blackBody.colors = colorRampPalette(c("black", "red", "orange","yellow","lightyellow"),space="rgb")

}

Struggling with mounting shared directory on VirtualBox

some good info

1) Run as sudo VBoxLinuxAdditions.run
1a) sudo sh ./VBoxLinuxAdditions.run
2) make directory e.g. HostData in /home/d3m629/ folder
3) Set what is shared is VirtualBox itself
4) sudo mount -t vboxsf -o uid=MYUSERNAME Google_Drive ~/HostData
5) then add this to /etc/init.d/rc.local or ? /etc/rc.local
5a) mount -t vboxsf -o uid=MYUSERNAME Google_Drive /home/MYUSERNAME/HostData
6) enter HostData directory and bookmark it for easy access.

Obviously MYUSERNAME has to be replaced with the actual one.


Another thing to do after installing Ubuntu on VirtualBox running on Mac is ...
Keyboard Layout -> Options -> Alt/Win Key behavior ->  Control is mapped to Win keys (and the usual Ctrl keys)

In case of Xubuntu.
Run
setxkbmap -option altwin:ctrl_win
To make the change permanent
echo -option altwin:ctrl_win >>~/.Xkbmap
original doc


Changing themes for Unity