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#28 Logarithmic coloring scheme

open
nobody
5
2007-07-06
2007-07-06
No

The current pixel coloring scheme (different colors for positive, zero, and negative) works well for log-ratios coming from microarray data. For other kinds of data, however, this coloring scheme may not be suitable. In our case, for example, all data are absolute and vary from a small positive value to a huge positive value. In this case, a logarithmic coloring scheme (such as available in GeneSpring) may be more appropriate. Here, the color is not based on the value itself, but on the logarithm of the value. Converting the data to logarithms before loading them into Java TreeView is not an optimal solution, since we would like to see the actual value (not the logarithm) when hovering over them with the mouse.

Discussion

  • Alok Saldanha

    Alok Saldanha - 2007-07-13

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    I gave it a short, have a look at version 1.1.1 to see if this is what you had in mind.
    Go to pixel setting and check log scale. The contrast will then be in units of fold change (log base 2), but you can "center" it (effectively pre-dividing by a constant") around values other than one.

     
  • Nobody/Anonymous

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    Thanks Alok!

    On my computer, it looks fine. But on my colleague's computer, we got an error when starting Java TreeView. I copied the error message below. I am not sure why we got the error on her computer but not on mine. Both are Windows machines. If it's an array out of bounds exception, as the error seems to indicate, I would expect the same error on my machine. Anyway, this is the traceback:

    C:\Program Files\Stanford University\Java TreeView>java -jar TreeView.jar
    Plugin Jar jar:file:/C:/Program Files/Stanford University/Java TreeView/plugins/
    Dendrogram.jar!/
    Registering Plugin Dendrogram
    Registering Plugin Alignment
    Registering Plugin KnnDendrogram
    Plugin Jar jar:file:/C:/Program Files/Stanford University/Java TreeView/plugins/
    Karyoscope.jar!/
    Registering Plugin Karyoscope
    Plugin Jar jar:file:/C:/Program Files/Stanford University/Java TreeView/plugins/
    Scatterplot.jar!/
    Registering Plugin Scatterplot
    Plugin Jar jar:file:/C:/Program Files/Stanford University/Java TreeView/plugins/
    Treeanno.jar!/
    Registering Plugin ArrayTreeAnno
    Registering Plugin GeneTreeAnno
    Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 5
    at edu.stanford.genetics.treeview.plugin.dendroview.ColorPresetEditor$PresetEditPanel.initialize(Unknown Source)
    at edu.stanford.genetics.treeview.plugin.dendroview.ColorPresetEditor$PresetEditPanel.access$000(Unknown Source)
    at edu.stanford.genetics.treeview.plugin.dendroview.ColorPresetEditor.synchronizeFrom(Unknown Source)
    at edu.stanford.genetics.treeview.plugin.dendroview.DendrogramFactory.setGlobalNode(Unknown Source)
    at edu.stanford.genetics.treeview.core.PluginManager.pluginAssignConfigNodes(Unknown Source)
    at edu.stanford.genetics.treeview.app.LinkedViewApp.scanForPlugins(Unknown Source)
    at edu.stanford.genetics.treeview.app.LinkedViewApp.<init>(Unknown Source)
    at edu.stanford.genetics.treeview.app.LinkedViewApp.main(Unknown Source)
    at LinkedView.main(Unknown Source)

     
  • Alok Saldanha

    Alok Saldanha - 2007-07-13

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    I'm glad to hear it's close, there's a lot of annoying detsils left, such as exporting scale bars.
    Regarding your colleague's exception, it looks like an issue with the global config file, which is called jtview.xml, and should be located in what windows considers your home directory. on my machine, this was c:\documents and settings\{username}.
    Renaming or deleting the file should fix the problem, but will also delete global preferences. If there is no confidential information in the file, and if this fixes the problem, I would appreciated it if you could email the file to alokito@users.sourceforge.net so I can figure out what caused the problem.

     
  • Nobody/Anonymous

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    Thanks, Alok!

    It turned out that jtview.xml was indeed the problem. The offending line in jtview.xml is in this section:

    <PluginGlobal name="Dendrogram">
    <ColorPresets default="5">
    <ColorSet name="RedGreen"/>
    <ColorSet up="#FEFF00" down="#1BB7E5" name="YellowBlue"/>
    </ColorPresets>
    </PluginGlobal>

    My correct jtview.xml does not have the 'default="5"' after ColorPresets; my colleague's jtview.xml did. If I add 'default="5"' to my jtview.xml, starting Java TreeView on my computer gives the same error message as she was getting with her jtview.xml. After removing jtview.xml from her computer, Java TreeView runs fine.

    Thanks again,

    --Michiel

     

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