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Merge pull request #2 from KlasJoenssson/UppdateCheatSheet
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Updated the cheat sheets
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@goglepox
goglepox committed Mar 22, 2012
2 parents c68bb8b + 269d01f commit e0ee01d
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110 changes: 64 additions & 46 deletions plugins/net.bioclipse.qsar.ui/cheatsheets/qsar-r.xml
View file
@@ -1,48 +1,66 @@
<?xml version="1.0" encoding="UTF-8"?>
<cheatsheet
title="Using QSAR data in R<intro>
<description>
This tutorial demonstrates how to use R to analyze QSAR. Note that R is experimental and must be installed from the experimental update site before following this tutorial.
</description>
</intro>
<item
title="Step 1: Open the R Console">
<description>
If you have R installed, then installing the Bioclipse-R Intergration feature let you access R directly from Bioclipse via the R-console.
Reveal the R-console from the menu <b>Window > Show View > Other</b> and select <b>R Console</b>.
</description>
<command
required="false"
serialization="org.eclipse.ui.views.showView(org.eclipse.ui.views.showView.viewId=net.bioclipse.r.ui.views.RConsoleView)"/>
</item>
<item
title="Step 2: Load the dataset into R">
<description>
Loading the dataset into R can be achieved by entering, in the R Console:<br/><br/>
<b>dataset &lt;- read.delim(file="myQsarProject/dataset.csv", sep=",", header=TRUE, row.names=1, na.strings="NaN")</b>
</description>
</item>
<item
title="Step 3: Use R to analyze dataset">
<description>
Here is a simple example to demonstrate how the read file can be analyzed in R:<br/><br/>
<b>dataset &lt;- as.matrix(dataset)</b><br/><br/>
<b>mod &lt;- lm(dataset[,1] ~ dataset[,2:ncol(dataset)], na.action=na.omit)</b><br/><br/>
<b>plot(mod)</b><br/><br/>
</description>
</item>
<cheatsheet
title="Using QSAR data in R">
<intro>
<description>
This tutorial demonstrates how to use R to analyze QSAR. Note that R is
experimental and must be installed from the experimental update site
before following this tutorial.
</description>
</intro>

<item title="Step 1: Open the R Console">
<description>
If you have R installed, then installing the Bioclipse-R Intergration
feature let you access R directly from Bioclipse via the R-console.
Reveal the R-console from the menu
<b>Window > Show View > Other</b>
and select
<b>R Console</b>
.
</description>
<command required="false"
serialization="org.eclipse.ui.views.showView(org.eclipse.ui.views.showView.viewId=net.bioclipse.r.ui.views.RConsoleView)" />

</item>

<item title="Step 2: Load the dataset into R">
<description>

Loading the dataset into R can be achieved by entering, in the R
Console:
<br />
<br />

<b>dataset &lt;- read.delim(file="myQsarProject/dataset.csv",
sep=",", header=TRUE, row.names=1, na.strings="NaN")</b>

</description>

</item>

<item title="Step 3: Use R to analyze dataset">
<description>

Here is a simple example to demonstrate how the read file can be
analyzed in R:
<br />
<br />

<b>dataset &lt;- as.matrix(dataset)</b>
<br />
<br />
<b>mod &lt;- lm(dataset[,1] ~ dataset[,2:ncol(dataset)],
na.action=na.omit)</b>
<br />
<br />
<b>plot(mod)</b>
<br />
<br />

</description>

</item>


</cheatsheet>
4 changes: 2 additions & 2 deletions plugins/net.bioclipse.qsar.ui/cheatsheets/scripting_qsar.xml
View file
Expand Up @@ -57,14 +57,14 @@
<b>qsar.calculate(molecules, descriptors)</b><br/><br/>

The gist 95189 shows a script to demonstrate this. To run it; just save it as a JavaScript,
e.g. as &qt;qsar-multi.js&qt;. Then open the file and run it.
e.g. as &quot;qsar-multi.js&quot;. Then open the file and run it.

</description>

<action
pluginId="net.bioclipse.scripting.ui"
class="net.bioclipse.scripting.ui.actions.ScriptAction"
param1="ui.open(gist.download(95189))"/>
param1="ui.openFiles(gist.download(95189))"/>

</item>

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