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Profile_r_heatmaps_instructions

Congratulations!

You have successfully installed http://profiles.tiki.org/R_HeatMaps, with a new menu on the side column to ease the navigation tasks. This R package allows the creation and edition of HeatMap graphics (as used in Bioinformatics) through a simple web interface. You can see the slides of a presentation in UseR2011 where Easy Web HeatMaps is shown (slideshow embbeded below as a slideshare presentation).

Environment ready?

1. Is PluginR installed?

If you see a series of numbers from 1 to 10 below, this means that you have your https://doc.tiki.org/PluginR already installed successfully in your Tiki site.
{R()}1:10{R}
Otherwise, you need to install PluginR as admin by means of:
  • tiki-mods.php (tiki-mods.php?action=install&package=wikiplugins-r) through the Tiki interface to install mods (see it in section 'Wiki plugins' at the bottom of the list).
    Or alternatively, install manually by
  • downloading PluginR from http://mods.tiki.org , decompressing it locally, and uploading the folders to their equivalent folders in the server side.

2. Are the dependencies in R packages installed?

{RR()}
      1. Chunk 1: Installation of easyHeatMap package and dependencies

          1. NOTE:
  1. * You need a few packages: install the ones you are missing in the central server location for R packages.
  2. * In this example we install them with this params: lib="/usr/lib/R/site-library", repos="http://ftp.heanet.ie/mirrors/cran.r-project.org/"
  3. but adapt the server paths or urls to your specific case
  4. * Remember you can install packages:
  5. * from the terminal with some command like:
  6. R CMD INSTALL /home/foo/myPackage.tar.gz --library="/usr/lib/R/site-library"
  7. * or from an R session with something like:
  8. install.packages(pkgs="/home/foo/myPackage.tar.gz", lib="/usr/lib/R/site-library", repos="http://ftp.heanet.ie/mirrors/cran.r-project.org/")

          1. Install the following required dependencies if needed in the central server location
          2. so that they can be reached by the webserver user (www-data, etc)
cat("Cheacking dependencies:\n")
if (is.na(match("gplots", installed.packages()))) {
install.packages("gplots", repos="http://ftp.heanet.ie/mirrors/cran.r-project.org/")
} else {
cat(" Package gplots is already installed. OK.\n")
}
if (is.na(match("gtools", installed.packages()))) {
install.packages("gtools", repos="http://ftp.heanet.ie/mirrors/cran.r-project.org/")
} else {
cat(" Package gtools is already installed. OK.\n")
}
if (is.na(match("gdata", installed.packages()))) {
install.packages("gdata", repos="http://ftp.heanet.ie/mirrors/cran.r-project.org/")
} else {
cat(" Package gdata is already installed. OK.\n")
}
if (is.na(match("caTools", installed.packages()))) {
install.packages("caTools", repos="http://ftp.heanet.ie/mirrors/cran.r-project.org/")
} else {
cat(" Package caTools is already installed. OK.\n")
}
if (is.na(match("easyHeatMap", installed.packages()))) {
##### Install the package "easyHeatMap"
### for the time being you can fetch it from:
### https://ueb.ir.vhebron.net/files/easyHeatMap_1.18.tar.gz
### or
### http://dl.dropbox.com/u/24830595/easyHeatMap_1.18.tar.gz
cat("Attempting to download easyHeatMaps from http://ueb.ir.vhebron.net/files/easyHeatMap_1.18.tar.gz \n")
download.file("http://ueb.ir.vhebron.net/files/easyHeatMap_1.18.tar.gz", "./easyHeatMap_1.18.tar.gz")
cat("Attempting to install package easyHeatMaps \n")
install.packages(pkgs="easyHeatMap_1.18.tar.gz")
if (is.na(match("easyHeatMap", installed.packages()))) {
cat(" Something must have gone wrong, since the package didn't get successfully installed for some reason")
} else {
cat(" Package easyHeatMaps successfully installed. \n You can now proceed to create some <a href=\"tiki-index.php?page=HeatMaps&cookietab=2\">HeatMaps</a>")
}
} else {
cat(" Package easyHeatMap is already installed. OK.\n")
cat("\n You can now proceed to create some <a href=\"tiki-index.php?page=HeatMaps&cookietab=2\">HeatMaps</a>\n")
}

{RR}


Help
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  • Official documentation of PluginR - html
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  • Presentation in UseR2011 where Easy Web HeatMaps is shown
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