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GO Distribution Chart

Contents

  1. Description
    1. Special notes
  2. Usage by Example
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Description

This plugin gives pie charts or bar charts of GO distribution of user-specified GO nodes with respect to a user-specified user node. For example, Fig. 1 is a pie chart for first level GO terms under molecular function by counting the number of genes in human chromosome 18, and Fig. 2 is the corresponding bar chart.
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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 by Example

  1. File -> Load, open the file "humanGene.tree"
  2. Plugins -> GO Distribution Chart. A window called "GO Distribution Chart" will appear.
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    Fig. 3

  3. In this example, we are trying to observe the GO distribution of first level GO terms under molecular function. To this end, we have to assign the GO terms that we want to observe. Select first level GO terms under molecular function, click mouse right button, then select "Added to GO Distribution Chart". Added GO terms will be listed in the table of Data Distribution Chart window (Fig. 4, blue rectangle). This list can be cleared by clicking the "Clear list" button (Fig. 4, green cycle), and a column can be deleted by selecting a cell and clicking the "Delete column" button (Fig. 4, blue cycle).
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    Fig. 4

  4. The main function of this plugin is to make charts according to the the GO distribution of nodes listed in the table. For example, the GO distribution is marked by the green color in Fig. 5, and the pie chart in Fig. 6 is made according to this GO distribution. Recall that the GO distribution in the GO tree is computed for all data by default, so it won't be changed until you enter the tracing mode. In order to display the GO distribution for a specified chromosome, be sure that Option -> Tracing is checked. Perform Tools -> Reset if necessary. The corresponding pie chart will be shown after clicking any chromosome node.
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    Fig. 5 Fig. 6

  5. By selecting "Bar chart" (Fig. 7, blue cycle), a bar chart will be shown according to the same numbers.
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    Fig. 7

  6. Other functions include:
    1. File -> Save table: Save listed information in the table.
    2. File -> Save figure: Save the chart.