R classes with references resources

https://stat.ethz.ch/R-manual/R-devel/library/methods/html/refClass.html
http://adv-r.had.co.nz/OO-essentials.html
https://www.bioconductor.org/help/course-materials/2010/HeidelbergNovember2010/ReferenceClasses-Morgan.pdf

or type in R
?ReferenceClasses

Building Crux

Quite straightforward. Otherwise well documented here:
http://cruxtoolkit.sourceforge.net/install-tutorial.html

You will need wget with ssl and https. I got mine from :
https://eternallybored.org/misc/wget/


Running comet with crux?

Beware! crux comet and comet have different interfaces.

Comet - you can download from here:
http://comet-ms.sourceforge.net/

R Package Quantable

New package quantable on CRAN:

Methods which streamline the descriptive analysis of quantitative matrices.

https://cran.r-project.org/web/packages/quantable/index.html

Has some routines to simplify various plots (i.e. qqplot) for multivariate data. 

Also a nice volcano.

Most up to date version can be found here:
https://github.com/protViz/quantable

Converting sql database schemas

After some thinkering I believe the best way to cope with various DB providers is to use an ORM.
I did try python SQLAlchemy.
At every corner I run into performance problems with python.



I might post an update on it in the near future.

mysql -> sqlite3
postgre -> sqlite3

CREATE  TABLE IF NOT EXISTS `pyMS`.`feature` (
  `feature_id` VARCHAR(40) NOT NULL ,
  `intensity` DOUBLE NOT NULL ,
  `overallquality` DOUBLE NOT NULL ,
  `quality` DOUBLE NOT NULL ,
  `charge` INT NOT NULL ,
  `content` VARCHAR(45) NOT NULL ,
  `msrun_msrun_id` INT NOT NULL ,
  PRIMARY KEY (`feature_id`, `msrun_msrun_id`) ,
  UNIQUE INDEX `id_UNIQUE` (`feature_id` ASC) ,
  INDEX `fk_feature_msrun1` (`msrun_msrun_id` ASC) ,
  CONSTRAINT `fk_feature_msrun1`
    FOREIGN KEY (`msrun_msrun_id` )
    REFERENCES `pyMS`.`msrun` (`msrun_id` )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION)
ENGINE = InnoDB;

CREATE  TABLE IF NOT EXISTS `feature` (
  `feature_id` VARCHAR(40) NOT NULL ,
  `intensity` DOUBLE NOT NULL ,
  `overallquality` DOUBLE NOT NULL ,
  `quality` DOUBLE NOT NULL ,
  `charge` INT NOT NULL ,
  `content` VARCHAR(45) NOT NULL ,
  `msrun_msrun_id` INT NOT NULL,
  CONSTRAINT `fk_feature_msrun1`
    FOREIGN KEY (`msrun_msrun_id` )
    REFERENCES `msrun` (`msrun_id` )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION);
CREATE UNIQUE INDEX `id_UNIQUE` ON `feature` (`feature_id` ASC);
CREATE INDEX `fk_feature_msrun1` ON `feature` (`msrun_msrun_id` ASC);

R plotting also with d3.js

R and d3.js

ggplot cheat sheet

http://zevross.com/blog/2014/08/04/beautiful-plotting-in-r-a-ggplot2-cheatsheet-3

Scatterplots with lattice

http://www.stat.ubc.ca/~jenny/STAT545A/block09_xyplotLattice.html

interesting links

http://blog.ae.be/combining-the-power-of-r-and-d3-js/
https://plot.ly
http://dimplejs.org/

If you are comfortable with GitHub, I wrote this tutorial about configuring GitHub to display webpages without using a third party site as supporting material for another course

https://github.com/thoughtfulbloke/appleorange
http://bl.ocks.org/

http://rawgit.com/

Windows tooling

Depends http://www.dependencywalker.com/
SysinternalsSuite https://technet.microsoft.com/en-us/sysinternals/bb842062.aspx

Building Pwiz is nonstandard ....

checkout 

svn checkout --username=witek96 svn+ssh://witek96@svn.code.sf.net/p/proteowizard

/code/trunk proteowizard-code

Download msparser from the matrixscience website...

tar jxf msparser_2_5_2_x86_linux64.tar.bz2

On Linux

./quickbuild.sh -j4 toolset=gcc --msparser-path=/home/witold/prog/msparser/gnu variant=debug pwiz_tools/BiblioSpec > log.txt

./quickbuild.sh -j4 toolset=gcc variant=debug pwiz_tools/BiblioSpec > log.txt

./quickbuild.sh -j4 toolset=gcc --msparser-path=/scratch/wolski/msparser/gnu

with prefix directory:

 ./quickbuild.sh -j4 --i-agree-to-the-vendor-licenses --msparser-path=/scratch/wolski/msparser variant=debug pwiz_tools/BiblioSpec --prefix=/scratch/wolski/pwizbuild

On Windows

With --msparser-path set

win 64

quickbuild.bat toolset=msvc-12.0  address-model=64  --i-agree-to-the-vendor-licenses --msparser-path=C:\Users\Wolski\Downloads\msparser2_5\vs2013 variant=debug pwiz_tools/BiblioSpec > log.txt

please not that I did specify pwiz_tools/Bibliospec as the build target..

win 32

just do not specify the address-model

.

Update : 12/10/2015 - building all of pwiz

quickbuild.bat  --i-agree-to-the-vendor-licenses toolset=msvc-12.0  -j8 --hash --without-compassxtract --msparser-path=C:\Users\Wolski\Downloads\msparser2_5\vs2013 optimization=space secure-scl=off address-model=64 variant=release

Further pwiz build options

debug

runtime-debugging=on

--without-binary-msdata (make sure to run clean.bat before this one)

quickbuild -j4 --i-agree-to-the-vendor-licenses --abbreviate-paths pwiz_tools/Bumbershoot/myrimatch//install
quickbuild -j4 --abbreviate-paths pwiz_tools/Bumbershoot/myrimatch//install


Some more ways to build Bumbershoot :) 

quickbuild.bat --i-agree-to-the-vendor-licenses -j4 --abbreviate-paths address-model=64 pwiz_tools/Bumbershoot

How to run clean on pwiz/pwiz directory?

there is a clean.bat file

Installing pwiz headers and libraries for use in other projects:

• I am just in the process to experiment with this command lines: 

quickbuild.bat libraries --libdir=<path to blib>\win\lib --includedir=<path to blib>\src\extern\proteowizard\install\include

quickbuild.bat toolset=msvc-12.0  address-model=64  --i-agree-to-the-vendor-licenses libraries --prefix=C:\Users\wolski\prog\pwiz-libraries-64

 ./quickbuild.sh -j4 --i-agree-to-the-vendor-licenses --msparser-path=/scratch/wolski/msparser variant=debug pwiz_tools/BiblioSpec --prefix=/scratch/wolski/pwizbuild