This refers to quantitative tracks displayed in genome heatmap. Below is a complete list of steps of selecting tracks to be displayed in genome heatmap. Click on link to view details about each step.
Tracks from different sources are grouped into "data sets", e.g. the track from Roadmap Epigenomics Project or ENCODE are in their own groups.
At the control panel, go to "Tracks" > "Heatmap tracks". You can find the "Data sets" panel folded by default:
click on the oval button to unfold it:
There's 3 data sets in above screen shot. Each is presented with logo, name, URL, and short description. The "in use" or "not in use" oval box indicates whether the data set is in use. And here only the "Roadmap Epigenomics Project" data set is in use.
To use the ENCODE data set, check its checkbox:
Press button, the ENCODE data set will be loaded and the oval will turn green:
Loading a data set retrieves track names and metadata from server. The tracks will be presented in track selection panel for user to choose.
Track selection panel organizes tracks in a structured way to make selecting track easy. By default it uses text tree to organize tracks:
Each line is a metadata term, and tree structure is defined by metadata vocabulary. Click on term names will fold/reveal its children terms:
The pair of numbers following each term name is number of tracks annotated by this term. Green is for total number, and red is number of currently displayed tracks in this group. Click the number, a new panel will be displayed in floating toolbox for you to make selection:
This panel contains the list of tracks from the number just clicked. Click letter "i" following track name to see detailed information on each track. Checkboxes in front of track name indicates this track is not been displayed. Check it and will mark the track for submission. "✕" means the track is been displayed. Click on it will remove it from display, and ✕ will be replaced by a checkbox.
Click button to check and mark all tracks for submission, click button to undo. Click button will remove any track from display in this list.
When you've checked any checkboxes, the "Heatmap tracks to be added" panel will be displayed below "Choose track" panel, in which each line corresponds to a marked track in "select heatmap track" panel:
Press button will add the list of tracks for display. Before you hit the button, you can keep this panel open and navigate to other places in the track selection panel and add tracks from other metadata terms. Once done, you can add them all in one time.
Finally, the content of "track selection" text tree can be changed by selecting different subsets of metadata vocabulary. Go to "Configure" panel on top of "track selection panel":
Change the drop-down menu marked as "Row" to "Assay" (leave the other unchanged), press button and the text tree will be composed by assay types:
A table or "grid" can be made for track selection panel instead of text tree. Following instructions above, change the second drop-down menu marked as "Column" into "Sample" in "configure" panel:
This will change the track selection panel into a large grid with rows made of "Assay" terms and columns of "Sample" terms:
Only part of grid is shown. You can quickly fold the grid by clicking yellow and blue stripes with words "Sample" "Assay" in them:
Same kind of number pairs are printed at cells of the grid where tracks are annotated to combination of terms. Click on the number pairs to carry out track selection as described above.
A shortcut exists to select all tracks within a row or column. Hover cursor above term names, a small menu with two options will appear by the term name. Select the "Select all" option, all tracks within the indicated row/column will be brought up for display.
Track informationright click on a track in genome heatmap,
click the "Information" option in the menu.
Track information in the form of key-value pairs will be displayed in a new panel in floating toolbox:
Configure track rendering See chapter genome heatmap for details.
Inter-track correlation right click on the intended track and select "Correlation" option. See chapter correlation for details.
Bird's eye view right click and select corresponding option. See chapter bird's eye view for details.
Remove tracks right click on genome heatmap and select "Remove" option to remove one single track. Right click on metadata color map to remove a group of tracks. And you can use the two buttons at bottom of "Heatmap track" panel to remove all tracks at once.
Display your own data See chapter custom bigWig track for details.
Last modifed: 12/24/2011