Creating and Customizing Scatter Plots

How to create and customize a 2D scatter plot on the BioBox platform

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  1. Create a project and create an "Analysis" within your project.
  2. Select " Visualizations" , under the differential expression tab, select 2D scatter next to the file you would like to work with. This will take you to the data table. Use the  drop down arrows next to column headers in the data table to filter and subset your data.
  3. Select the "Plot" tab, this will take you to the scatter plot that be customized and configured.  Use the plot customization panel located on the right side of your plot to customize and configure your plot. 
    1. Series.  Specify the data from your file that you would like plotted on your X and Y axis. Add tooltips such as gene, fold change and p value so that this information is displayed as you hover over data points in your plot.  If you select "invert plot- display -log10Pvalue, this will display the -log10 of the values on your Y axis. It is important to ensure you have the P values or the adjusted P valued displayed on the Y axis if you wish to do this. 
    2. Grid. Under the grid menu you can customize your chart title, add/ remove gridlines and the zoom slider. 
    3. Axis. The axis menu allows you to fully customize the X and Y axis with minimum/ maximum values, axis titles, font size, location and more. 
    4. Visual Customizations 5: 52 .  This enables you to customize the colour and shape appearance of data points.   Customizations are applied in groups, each group is subsetted on the basis of criteria in your dataset e.g. log2fold change, p value etc. 
      1. Under the Visual Customization menu, select " add a group" 
      2. Within the customization dialog, specify the dimension (criteria from your dataset you would like the customizations to be applied on the basis of).  You can specify 1-2 dimensions maximum. 
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      3. Select "Appearance" to update the colour, shape, and labels associated with data points in your group. 

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      1. Single data point customizations. To customize a single data point, right click on a data point and  a customization dialog will appear.  You can update the colour, shape, and label associated with each individual data point.  To add a label like a gene name, select the " add data label" checkbox  and customize what you would like to display in the label.  If you would like to remove the annotation, right click on the data point and deselect "show data label". 

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You can apply as many group and single data point customizations to your plot as you would like. Select the edit icon next to the group to update the properties associated with your groups.

When you are satisfied with your plot select the cloud icon in the top right hand corner of the plot to export it. During export you can customize plot height, width, file type and resolution. If ant of these properties are updated you will see a preview of the updates prior to export.

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All changes that you make to your plot are automatically saved, this is reflected in the analysis tool bar located in the top right hand of your analysis.