Genome contact map browser

It is an application to browse genome contact maps along with respective genomic track datasets. It acts as an interactive visualizer, where user can browse the data by dragging and zooming.

To launch browser, execute following command:
gcMapExplorer browser
Screen snapshot of Genome Contact Map browser

Genome Contact Map browser

  1. Click on arrow to move the maps in respective directions. The genomic datasets also follow automatically.
  2. Click on these buttons to zoom in and out. The genomic datasets also follow automatically.
  3. Use this to go to on specific coordinate. Input can be real or indexed coordinate.
  4. Change width-spacing between plots.
  5. List of all plots. Active plot is selected. One can select a plot to make it active.
  6. Reset all maps to original view.
  7. Display information of current resolution and unit shown in plots.
  8. Name of contact map. Usually chromosome name.
  9. Various options. Presently shown for color mapping and scaling of maps. It can be used to modify colormaps, color scaling range and color scaling type.

Add a genomic track dataset

Click on File -> Add genomic dataset to ... and select the contact map for which new dataset is need to be added. A new window will appear where user may select a compatible file by clicking on Open button. Afterwards, different box will appear depending on the input file format.

  • h5 file: User is prompted to select the dataset.

    Screen snapshot of dataset selector

    Select genomic track dataset

    By default, the genomic track is added at the bottom of map. However, one can select top in the above dialog box to plot the track at the top of the contact map.

  • bigWig/wig/bed file : Since, only h5 files are compatible with browser, a window will appear as similar to h5Converter to convert these files to h5 on the fly. By default, the generated h5 file will be deleted after use because Remove is checked. To save the generated h5 file, uncheck Remove option and change location of output file.

    Once dataset is converted, user is prompted to select the dataset as shown above for h5 input file.

    To reduce the waiting time for conversion process, only dataset for the required chromosome is converted. When later another chromosome is selected in browser, h5Converter will again appear and dataset will be again converted for the selected chromosome. Once dataset for a chromosome is converted, it remains stored in the h5 file. Therefore, when this chromosome is re-selected in browser, no conversion is required and dataset is plotted in browser instantly.

    Note

    The options in h5Converter are only editable at first time. Later when another chromosome is selected in browser, this box will again appear, however, options will not be editable.

Change page size and orientation

Click on Edit -> Change Page Size and select desired page size. In case of custom page size, click on Custom. A dialog will open, where user can specify new page size.

Screen snapshot of page size dialog

Change Page Size Dialog

Save as image

Click on File -> Save Plot, choose file name with acceptable extension and click on Save button to save the plot as image file.

Change Genomic track plot setting

Select a Genomic Dataset Y-Scaling option in Settings at right panel. Below several options will appear. These include color, line width, maximum and minimum limit along Y-axis.

Screen snapshot of genomic track options

Change Genomic track plot options

Change marker setting

Select a Marker option in Settings at right panel. Below options will appear to modify the marker settings.

Screen snapshot of marker settings

Change marker settings

User defined colormap

Although several colormap is already included in the browser. One may generate own colormap and later modify it using the implemented option. To open this, click on Edit -> Add/Modify colormap.

Screen snapshot of colormap dialog box

Add/Modify colormap

This box can be used to create or modify the colormaps. The shown colormap can be saved as a text file for later use.

Modify Axis Properties

Properties of both X and Y axis are highly customizable. User may customize most of the properties such as font, tick-lengths, axis-labels etc. To open this box, right click on plot and choose the axis properties.

Screen snapshot of Axis Properties interface in Browser

Axis Properties interface in Browser