Bird's Eye View

The Bird's Eye View function has been re-designed and is described here.

As usual, to invoke this function on a heatmap track, right click on that track in heatmap, and choose corresponding option:

The Bird's Eye View will be displayed in a new panel above existing page contents:


Most catchy is the wiggle plot of track data. Individual plots are generated for each chromosome, with chromosome ideogram shown below. Chr name and length is printed on left.

If an interesting region is spotted, you can quickly zoom into it by dragging on the chromosome ideogram graph:

Hover pointer over the wiggle plot will generated a small tooltip indicating the name of the track. Left-click the wiggle plot will display details of this track in floating toolbox (this is useful to discern from multiple tracks plotted together, as shown later):

To configure rendering style of the wiggle tracks, right click to get the panel like below:

Change bar color by clicking on the color blocks, where value above/below threshold will be colored differently:

Drag on the downward-pointing arrow to change threshold:

And change track height via the drop down menu.


Above options apply to individual track. Other non-track-specific options are available via the big wrench icon:

Here you can change plot width, toggle display of chromosome ideogram, and viewbox height. By changing plot width, all the tracks will be recomputed on server and this is likely to take a bit of time.

The Bird's Eye View allows displaying multiple tracks in same view. To do this, close the panel and back at browser view. Add another track in same way:

The newly added track is in default color. Configure its style in same way as described above.

All displayed tracks are registered in the white-background table with name "Computed tracks". The display of the table can be toggled by clicking on the image button above it. Each row is one track with track name in it. In front of name is a checkbox, you can check/uncheck it to show/hide that track from display. Hide-and-show a track won't involve server-interaction as the data is cached on client side.

And you can configure style of all tracks in one place using the wrench icon at bottom-right corner of "computed tracks" table.


So above summarized the newly finished Bird's Eye View function. A list of features has been scheduled in my job queue, and you're welcome to suggest more!

1. display genomic feature density
2. display analysis results (pairwise comparison and hypothesis test)
3. compute correlation analysis on tracks in bird's eye view

Floating toolbox remodeled

The floating toolbox has just got a new look:

The message console is still there. On top of that are buttons arranged in two rows. The first row is for panning and zooming. The magnifiers with +/- in it are for zoom in/out. The size of icon from small to big indicates magnitude of zooming.

The « » signs are for panning. Clicking on it will shift currently displayed region to left/right one screenful at a time. Although in most cases you do panning by dragging on heatmap canvas, this complements one funny situation when no tracks are displayed in heatmap -- which means, you have nowhere to drag on! And I hope this can enable panning on touch screen devices. Let me know if it works or not.


Buttons in the second row will invoke various "apps". You're free to click them and none of them will take you away:

• ? (smaller question mark): help message ballons
• ? (bigger question mark): user manual
• ♞: shows relocation options (jump to genes, etc)
• sticky note icon: generates one sticky note
• eye icon: opens the Bird's Eye View panel

Sticky note

The *paperless* sticky note is available now! You can create notes and place on any corner of Browser page as a reminder of anything.

First, go to floating toolbox:

Click "more" button to reveal the contents, where you can find the "make sticky note" button:

Click that button will generate a small note at a random place on the page:

By default the note is read-only. You can drag and move it.

If you mouse over the note, two little buttons will appear at top right corner:

Click ✎ to edit the note, and click ✔ to save:

If you've written too many lines, drag on the bottom right corner to resize the note:

Finally drag on the note to move around when you're not editing. Click X to delete note.

But this function is still experimental... Mike Steve requested this feature. However it's not functioning properly on his computer (Mac+firefox)! But it does run on other similar machines... Let me know the problems and I will try to fix any bugs there.


In the future the sticky notes you created might be saved under session. Now your sticky notes CAN be saved under session.


Update: It turned out that web browser plugins that manipulates <textarea> would disrupt functioning of sticky note. User has to disable the plugin to use the function or there's no other way round currently.

Heatmap configuration

The heatmap track configuration function has been adjusted a little bit. Now if you right click on heatmap, you will get a menu like following:

Choose the wrench option and a small panel will appear in floating toolbox letting you to configure this track:

Here you can click on a color stripe to change coloring style of that track, drag the slider to change threshold percentage, and use the drop down menu to change height or convert it to wiggle plot.

Lastly, if you check the "apply to all heatmap tracks" checkbox, you will be configuring all tracks on display now. Uncheck it to go back to single track configuration.

During check and uncheck, the tracks that are subject to configuration will be highlighted by animated dash lines:

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Additionally, a small twist has been added to heatmap track selection panel, where you can click the color oval to expand/fold rows and columns: