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Data 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 counts of user-specified R-nodes that having a user-specified GO annotation. For example, Fig. 1 is a pie chart for genes in each human chromosome that having GO annotation "nucleic acid binding", 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 -> Data Distribution Chart. A window called "Data Distribution Chart" will appear.
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    Fig. 3

  3. In this example, we are trying to observe the distribution of genes in different human chromosome given a GO annotation. To this end, we have to assign the chromosomes that we want to observe. Select some chromosomes, click mouse right button, then select "Added to Data Distribution Chart". Added chromosomes 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, red cycle).
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    Fig. 4

  4. Click on any GO node in the GO tree. The main function of this plugin is to make charts according to the the number of selected descandent R-nodes (in this case, genes) of each node listed in the table. For example, the numbers of selected descandent R-nodes are the numbers marked by the green color in Fig. 5, and these numbers are used to make the pie chart in Fig. 6.
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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.