galaxy-central (ngs) / tools / plotting / scatterplot.xml

<tool id="scatterplot_rpy" name="Scatterplot">
  <description>of two numeric columns</description>
  <command interpreter="python"> $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab"</command>
    <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/>
    <param name="col1" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
    <param name="col2" type="data_column" data_ref="input" numerical="True" label="Numerical column for y axis" />
    <param name="title" size="30" type="text" value="Scatterplot" label="Plot title"/>
    <param name="xlab" size="30" type="text" value="V1" label="Label for x axis"/>
    <param name="ylab" size="30" type="text" value="V2" label="Label for y axis"/>
    <data format="pdf" name="out_file1" />
    <requirement type="python-module">rpy</requirement>
  <!-- TODO: uncomment the following test when we have tools.update_state() working for 
       multiple dependents with the same dependency.
      <param name="input" value="scatterplot_in1.tabular" ftype="tabular"/>
      <param name="col1" value="2"/>
      <param name="col2" value="3"/>
      <param name="title" value="Scatterplot"/>
      <param name="xlab" value="V1"/>
      <param name="ylab" value="V2"/>
      <output name="out_file1" file="scatterplot_out1.pdf" />

.. class:: infomark

**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*



This tool creates a simple scatter plot between two variables containing numeric values of a selected dataset. 

- All invalid, blank and comment lines in the dataset are skipped.  The number of skipped lines is displayed in the resulting history item.

- **Plot title** The scatterplot title
- **Label for x axis** and **Label for y axis** The labels for x and y axis of the scatterplot.



- Input file::

    1   68  4.1
    2   71  4.6
    3   62  3.8
    4   75  4.4
    5   58  3.2
    6   60  3.1
    7   67  3.8
    8   68  4.1
    9   71  4.3
    10  69  3.7 

- Create a simple scatterplot between the variables in column 2 and column 3 of the above dataset.

.. image:: ./static/images/scatterplot.png