History: Profile_r_heatmaps_instructions

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Source of version: 8 (current)

! 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 ~~grey:''(slideshow embbeded below as a slideshare presentation)''~~.
* http://ueb.vhir.org/2011+User

^ -=Environment ready? =-
!!# 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.
!!# Are the dependencies in R packages installed?
{RR()}
##################################################################
### Chunk 1: Installation of easyHeatMap package and dependencies
##################################################################

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

##### Install the following required dependencies if needed in the central server location
##### 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 =-
* Accepted parameters in the version of PluginR installed in this system
+ {FADE(label="Click HERE to view/hide them", icon="y")}{PLUGINMANAGER(plugin=r singletitle=none) /}{FADE}
* Official documentation of PluginR - html
+ {FADE(label="Click HERE to view/hide it", icon="y")}
^-=To see it in full size out of this frame, [http://doc.tiki.org/tiki-index_p.php?page=PluginR|click here]=-^
{IFRAME(name="Documentation of PluginR",width="100%",height="1000",align="middle",frameborder="0",marginheight="0",marginwidth="0",scrolling="auto",src="http://doc.tiki.org/tiki-index_p.php?page=PluginR")}{IFRAME}
{FADE}
* Presentation in UseR2011 where Easy Web HeatMaps is shown
+ {CENTER()}{HTML()}
<div style="width:425px" id="__ss_8883326"><strong style="display:block;margin:12px 0 4px"><a href="http://www.slideshare.net/ueb52/2011-use-rtikipluginr" title="2011 use r_tiki_pluginr">2011 use r_tiki_pluginr</a></strong><object id="__sse8883326" width="425" height="355"><param name="movie" value="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=2011usertikipluginr-110817100637-phpapp02&stripped_title=2011-use-rtikipluginr&userName=ueb52" /><param name="allowFullScreen" value="true"/><param name="allowScriptAccess" value="always"/><embed name="__sse8883326" src="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=2011usertikipluginr-110817100637-phpapp02&stripped_title=2011-use-rtikipluginr&userName=ueb52" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="355"></embed></object><div style="padding:5px 0 12px">View more <a href="http://www.slideshare.net/">presentations</a> from <a href="http://www.slideshare.net/ueb52">UEB</a>.</div></div>
{HTML}{CENTER}
^

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History: Profile_r_heatmaps_instructions

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History: Profile_r_heatmaps_instructions

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