1. How is the "data point value" computed
  2. Heatmap track rendering
  3. Configure heatmap track rendering
  4. Configure many tracks at same time
  5. Re-arrange tracks
  6. Display track names
  7. Add/remove tracks from genome heatmap

The genome heatmap

The Genome Heatmap is a panel at the center of Human Epigenome Browser. It is a container of tracks with quantitative data, and they will usually be displayed in form of heatmaps, though wiggle plots is also supported. The quantitative data can be of any type (gene expression, transcription factor binding, DNA methylation, ...), from any kind of experiments (microarray, sequencing, ...), and both positive and negative values could be represented. Inside the heatmap panel, usually one row corresponds to one experiment. When you move the cursor over the heatmap, a tooltip will pop out showing information about the track under the cursor, and the specific track score at that position. The genomic position of the point will also be given in the tooltip.

How is the "data point value" computed?

Above the genome heatmap there's brief text telling current status of the Browser:

The last line "One pixel spans 6250 base pairs" tells the length of genomic region each pixel spans in genome heatmap. Unless you are at sufficient zoom-in level, this number will always be > 1 and is likely to be a big one. As a result of such case, the track data over the pixel-spanned region is averaged into a single value, no matter whether the region is 6 bp, 6 kb, or 6 mb in length.

Heatmap track rendering

The color of a heatmap cell is used to represent its underlying track score. A threshold value is first determined via three possible ways described below. If the heatmap cell gets value of 5 while the threshold value is 10, the color of heatmap cell will be attenuated or lightened to reflect the difference. White color is used for baseline value zero. And if heatmap cell value is above threshold, then it will have a separate color.

Configure heatmap track rendering

The heatmap track can be configured in a few ways including plot color, Y scale, logarithm transform, and track height. Right-click on a track in genome heatmap to get the context menu:

Select "Configure" option, the configuration panel will appear in floating toolbox:

Plot color The two color blobs let you decide plot color for positive/negative values. Click on it, the color palette will appear near where cursor is. Choose a color from the palette, the blob will change its color accordingly. This color is used when data value is within the range between baseline and threshold value. See below for cases when you need to choose color for values beyond threshold value.

Y axis - automatic scale If there's positive values in the track data, max is used to set upper limit of Y scale. And if there's negative values, min is used for lower limit. And baseline of zero is used when there's only positive/negative values. All data values are within the range defined by Y axis.

Y axis - fixed scale When you choose this option, two text fields will appear where you enter numbers to be used as scale threshold: Once you entered the values, press button to let it take effect. Notice when using this option, additional color blobs appear inside original ones. Using the new ones you can determine the color for data values beyond threshold. Following is an example of setting dark red as "beyond threshold color", all heatmap cells with values above 30 will have dark red color:

Y axis - percentile threshold will compute the value of given percentile and use that value as threshold. This method is useful to prevent outlier values from screwing the view. When you choose this option, a ruler appears and let you select a percentile (slide the ↓ arrow, or click « »): Once a percentile value is selected, the track will update.

Let's look at a short example. Following is several MRE-Seq read density tracks rendered with automatic scale. Only a few regions have red color, the rest are all white. This is because read density is much higher in the red regions. But as low MRE-Seq read density still provides decent proof on unmethylation of CpG sites, we switch to percentile threshold and select 90 percentile: now the very high score are "masked" with dark red color, and many regions are now visible with lesser read density data.

Logarithm transformation Will take logarithm on track data. You can select one of three bases for logarithm. Following example shows taking logarithm on a group of tracks. Values below 1 will become negative and are thus plotted in blue.

Track height Use the drop-down menu to select a height. With small track height you can pack many tracks in one screen. Following is 118 tracks all in height of 2 pixels: Turning height ≥ 20 pixels will convert the track into wiggle plot, letting you better focus on them:

Configure many tracks at same time

Right-click on a color block in metadata color map which spans multiple tracks, and you'll be configuring appearance of these tracks at same time:

An option can be found at bottom of track configuration panel with words "apply to all tracks". Check it and you'll be configuring all tracks in genome heatmap.

Re-arrange tracks

A few different ways are available:

  1. Sort and rank tracks by correlation coefficient, refer to correlation analysis for details
  2. In metadata color map:
  3. Drag on the banded column on the right of metadata heatmap to move one track at a time.

Display track names

Yes. Look for button in browser configuration panel.

Add/remove tracks from genome heatmap

To see a list of curated tracks provided by Browser, refer to chapters on heatmap tracks. To display your own data, follow instructions on custom bigWig tracks.


Last modifed: 12/22/2011