tracks-wig.md

WIG track

• Display mode
• Scale mode
  • Manual scale
  • Auto-scale
  • Group scaling
• Track colors
• BedGraph tracks

WIG tracks can visualize information from wig of bigWig files.

At the demo site, bigWig files are used to show the coverage of BAM files.

When you hover over a location on a WIG track, the value for that location appears.

Display mode

NGB supports "Bar Graph" (default) and "Heat map" display modes for BigWig tracks.

If a "Bar Graph" display option is chosen – each BigWig’s coordinate is being shown as the bar, depending on the locus "value".
If a "Heat Map" display option is chosen – each BigWig’s coordinate is being shown with different color intensities, depending on the locus "value".

To change the display mode:

1. Click the hyperlink near the Display label in the BigWig track header:
   
2. In the list, select the display mode you wish, e.g.:
   
3. The display mode will be changed according to the selected one:
   

Also, the display mode can be changed for a group of selected BigWig tracks. For that:

1. Select several BigWig tracks.
2. Use the Display control in the floating menu of selected tracks:
   
3. Select the display mode.
4. In such case, the set display mode will be applied to all selected BigWig tracks:
   

Scale mode

NGB supports several scale modes for the BigWig tracks: Auto-Scale / Manual Scale, and also for both types the Log Scale can be applied additionally.

Manual scale option allows to set the absolute scale range for the track.
Auto scale option calculates the displayed data range automatically and apply this range to the track.
Log scale option allows to set logarithmic scale for the track.

Manual scale

To set the Manual scale:

1. Click the hyperlink near the Scale label in the BigWig track header:
   
2. In the list, select the Manual item:
   
3. In the popup, specify min and max values for the scale and confirm, e.g.:
   
4. The set scale will be applied:
   
5. If you wish to apply one the same manual scale to all alignments tracks in the browser - return at step 3 and set the "Apply to all alignments tracks" checkbox:
   
   In that case, all alignments tracks will have the same specified manual scale:
   
6. If you wish to apply one the same manual scale to all BigWig tracks in the browser - return at step 3 and set the "Apply to all WIG tracks" checkbox:
   
   In that case, all BigWig tracks will have the same specified manual scale.
7. If you wish to apply manual logarithmic scale to the track - return at step 3 and set the "Log scale" checkbox:
   
   In that case, for the current track the logarithmic scale will be applied (see the additional label appears near the vertical axis):
   

Auto-scale

To set the Auto scale:

1. Click the hyperlink near the Scale label in the BigWig track header:
   
2. In the list, select the Auto-scale item:
   
3. Necessary data range will be calculated automatically and applied to the track:
   
4. If you wish to apply logarithmic scale to the track - click the hyperlink Auto-Scale in the BigWig track header and set the "Log scale" checkbox:
   
   In that case, for the current track the logarithmic scale will be applied (see the additional label appears near the vertical axis):
   

Group scaling

To set the scale for a group, select several BigWig tracks and click the Scale item in the floating menu of selected tracks:

There are several scale modes for a group of BigWig tracks that can be set:

Auto scale option - for each selected track separately - calculates the displayed data range automatically and apply it for the track.
Manual scale option allows to set the absolute scale range that will be applied for all selected tracks simultaneously.
Group Auto scale option - for all selected tracks simultaneously - calculates the common displayed data range automatically and apply it for all tracks.
Log scale option allows to set logarithmic scale for all selected tracks.

Example of the Auto-scale for several tracks:

Example of the Manual scale for several tracks (configuration is the same as described above):

Example of the Group Auto-scale for several tracks:

Note: BigWig tracks with the Group Auto-scale are being colored with special indicator (near the scale axis) to let the user know which tracks have the same range applied.

Track colors

NGB supports the ability to change the BigWig track colors (depending on the value - positive/negative).

To customize colors of the BigWig track:

1. Click the General item in the track header.
2. Click the Color item in the list:
   
3. Click the color panel you wish to change, e.g.:
   
4. Pick a color within the special control:
   
5. Confirm changes:
   
6. Color changes will be applied:
   
7. If you wish to apply changed color scheme for all possible tracks in the browser - return at step 3 and set the "Apply to all tracks" checkbox.
   If you wish to apply changed color scheme for all alignment tracks in the browser - return at step 3 and set the "Apply to all alignment tracks" checkbox.
   If you wish to apply changed color scheme for all BigWig tracks in the browser - return at step 3 and set the "Apply to all WIG tracks" checkbox.

Also, you can manage the colors for a group of selected BigWig tracks. For that, use the General -> Color items in the floating menu of selected tracks:

In such case, the set color scheme will be applied only to selected tracks:

BedGraph tracks

NGB supports the uploading and reading of the BedGraph format.

Exposing the BedGraph files to the client is in the same manner as for the BigWig format.

For the BedGraph files, are supported:

• common tracks' features: selection, renaming, height resizing, label font resizing
• specific features: changing of the display mode, changing of the scale mode, changing of the track color