User:Timothee Flutre/Notebook/Postdoc/2011/11/07

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(Entry title: myheatmap)
(About R: add links helping in package dev)
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==Entry title==
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==About R==
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* '''Motivation''': when analyzing data for any research project, it's essential to be able to quickly clean the raw data, transform them, plot intermediary results, calculate summary statistics, try various more-or-less sophisticated models, etc. This must be easily doable with small as well as large data sets, interactively or not. Several tools exist to fill exactly this need, and [http://en.wikipedia.org/wiki/R_%28programming_language%29 R] is only one of them, but I especially recommend it because it is build by statisticians (this means that the implemented models are numerous and state-of-the-art). Moreover, it's [http://cran.r-project.org/sources.html open-source] (and even [http://www.r-project.org/about.html free software]), platform-independent, full of [http://cran.r-project.org/web/packages/available_packages_by_name.html packages], with [http://cran.r-project.org/web/views/ well-documented] resources, etc, so give it a try!
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* '''Documentation''':
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** try it [https://www.codeschool.com/courses/try-r online]
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** official introductory [http://cran.r-project.org/doc/manuals/R-intro.html manual]
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** well-organized [http://www.statmethods.net/ how-to]
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** freely-available [http://adv-r.had.co.nz/ book] for advanced usage
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** [http://www.r-bloggers.com/ aggregator] of R blogs
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** [http://gallery.rcpp.org/ gallery] of examples extending R with C++ via [http://www.rcpp.org/ Rcpp]
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** compatible with [http://ess.r-project.org/ ESS] ([https://openwetware.org/wiki/User:Timothee_Flutre/Notebook/Postdoc/2012/07/25 Emacs] mode), besides other IDEs such as [http://www.rstudio.com/ Rstudio]
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** but R language specifications are unconventional ([https://github.com/tdsmith/aRrgh aRgh], John Cook's [http://www.johndcook.com/R_language_for_programmers.html doc], [http://www.burns-stat.com/pages/Tutor/R_inferno.pdf R Inferno])
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* '''Tips''':
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** [http://menugget.blogspot.de/2013/01/my-template-for-controlling-publication.html procedure] for publication-quality plots
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** [https://sites.google.com/site/rosselldavid/home/tips tutorial] to debug within Emacs some C/C++ code called by R
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** make your own R package: [https://github.com/jtleek/rpackages policy] from Jeff Leek, [https://github.com/hadley/devtools devtools] from Hadley Wickham, [http://projecttemplate.net/ ProjectTemplate]
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* customize the built-in heatmap in R (inspired from [http://stackoverflow.com/questions/5687891/r-how-do-i-display-clustered-matrix-heatmap-similar-color-patterns-are-grouped/5694349 this]):
* customize the built-in heatmap in R (inspired from [http://stackoverflow.com/questions/5687891/r-how-do-i-display-clustered-matrix-heatmap-similar-color-patterns-are-grouped/5694349 this]):
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  myheatmap(mydata.sort)
  myheatmap(mydata.sort)
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Revision as of 01:41, 5 December 2013

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About R

  • Motivation: when analyzing data for any research project, it's essential to be able to quickly clean the raw data, transform them, plot intermediary results, calculate summary statistics, try various more-or-less sophisticated models, etc. This must be easily doable with small as well as large data sets, interactively or not. Several tools exist to fill exactly this need, and R is only one of them, but I especially recommend it because it is build by statisticians (this means that the implemented models are numerous and state-of-the-art). Moreover, it's open-source (and even free software), platform-independent, full of packages, with well-documented resources, etc, so give it a try!


  • customize the built-in heatmap in R (inspired from this):
S <- 3  # nb of subgroups
V <- 7  # nb of observations
z <- matrix(c(0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,0,1,1,1,0,0), nrow=V, ncol=S, byrow=TRUE)

myheatmap <- function(z, out.file="") {
  def.par <- par(no.readonly=TRUE)
  par(mar=c(4,5,3,2), font=2, font.axis=2, font.lab=2, cex=1.5, lwd=2)
  if (out.file != "")
    pdf(out.file)
  layout(mat=cbind(1, 2), width=c(7,1))  # plot +  legend
  mycol <- rev(heat.colors(4))
  image(x=1:NCOL(z), y=1:NROW(z), z=t(z),
        xlim=0.5+c(0,NCOL(z)), ylim=0.5+c(0,NROW(z)),
        xlab="", ylab="Observations sorted by cluster", main="Custom heatmap",
        axes=FALSE, col=mycol)
  axis(1, 1:NCOL(z), labels=paste("subgroup", 1:NCOL(z)), tick=0)
  par(mar=c(0,0,0,0))
  plot.new()
  legend("center", legend=sprintf("%.2f", seq(from=min(z), to=max(z), length.out=5)[-1]),
         fill=mycol, border=mycol, bty="n")
  if (out.file != "")
    dev.off()
  par(def.par)
 }

myheatmap(mydata.sort)


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