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ExpressionView

Contents

  1. Description
    1. Special notes
  2. Usage
    1. Special notes
  3. User data preparation
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Description

This plugin draws expression levels of given property nodes of type "exp" of selected representative nodes in the user tree. That is, you would see changes of expression levels of samples (Fig. 1) of a specific GO category if you set the appearance level to "Representative" (Fig. 2, the red rectangle).
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Fig. 1 Fig. 2

Special notes
  1. This plugin incorperates JFreeChart (1.0.0-pre2) for making charts.
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Usage

  1. Plugins -> ExpressionView plugin, for invoking the plugin window.
  2. This plugin draws all "selected" representative nodes, i.e., a representative node you click or representative nodes under the node you click. So it is suggested to set the appearance level to "Representative" (Fig. 2, the red rectangle).

  3. For the help window.
  4. For saving the expression plot.
  5. After every selection, this field shows an accession if only one representative is selected; otherwise, "Multiple selection".
  6. The plot will automatically adjust the range if "Auto" is selected; otherwise, you should input Y-Min and Y-Max by yourself.
  7. The plot will be in log-scale if "logY" is selected.
  8. Click "Memorize plot" for fixing current plot so that newer selections will be drawn in a different color and memorized plot will be shown at the same time.
  9. Click "Clear memory" for releasing the memorized plot.
Special notes
  1. Missing values of Representative nodes will be reported as 0.
  2. log-values of values less than or equal to 0 will be transferred as floor(log10(the minimum value greater than 0))-1.
  3. For a multiple selection, a thick line will be appended for representing the average.
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User data preparation

This section is for preparing the user data for visualization of this plugin. We strongly recommand you to read the file formats.

This plugin looks for property nodes of type "exp", where the content fields should be separated into two fields as "tags" and "expression valuess". All you need to do is to prepare node strings like "PR:exp:pphy2:0.09" for property nodes, and to add them to some tree.