Common Tasks

Peter Kerpedjiev edited this page Mar 21, 2017 · 23 revisions

Overview and Terminology

HiGlass (HG) is organized into multiple levels of display.

Website: The website that you are currently looking at.

App: The page that contains a fullscreen view of HG.

Container / Component: The part of the website that shows the actual HG views and tracks.

View: A collection of tracks that share common axes. Views can be linked by zoom.

Track: A region which contains plotted data. This can range from lines, gene annotations and axes on 1D tracks to heatmaps and annotations on 2D tracks.

Series: A set of data which is plotted in a track. Multiple series can be displayed in a single track. Each series requires a track in order to be displayed. A track cannot exist without any series.

Usage

Adding a new track

The most elementary task in HiGlass is adding a track. This can be done by clicking on the '+' sign of the view header and selecting where to add the new track. The list of available tracks is pulled from our server and filtered according to which datatypes can be displayed in this location. 2D data (heatmaps from cooler files) may be displayed either in the center, or on the edge tracks, where only the region near the diagonal will be shown. 1D data (e.g. from bigWig files) is limited to the edge tracks.

Each dataset can often be displayed in multiple ways. A 2D dataset can be displayed as a heatmap or as a rendering of the tiles which it is retrieved as. 1D datasets can [currently] be displayed as lines or as tile outlines. Gene annotations can be displayed as exon-intron plots or as tile ids.

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Resizing a view:

Individual views can be resized but they always expand to fill the available vertical space.

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Adding and removing views:

New views can be created by copying existing views. They can then be edited to display different data.

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Replacing tracks

A common task is to replace an existing track with a new track. This can be accomplished by either first closing the original track and then adding a new one in its place or simply selecting Replace track from a track's configuration menu:

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Changing a heatmap's colormap

The colormap for contact matrices can be changed from the 'track config' menu at the upper right corner of the heatmap. From there you can select from a number of preset color maps (afmhot, hot, jet ...):

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These presets roughly correspond to the some of the examples available from matplotlib and are defined in the file app/scripts/config.js.

Custom color map values can also be set by selecting 'Custom ...':

Adding track labels

Track labels display the name of the dataset being displayed. Note that at the moment having multiple series will lead to overlapping labels. This will be fixed in future releases.

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Adding horizontal heatmap tracks

Click the 'plus' icon in the upper right corner:

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Pick the location where you want it displayed:

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Pick a dataset:

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Pick the way you want to display it (for a heatmap in the 'top' position, there's currently only one option: 'horizontal-heatmap')

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After clicking 'submit', you should see the new dataset:

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You can then flip it by changing its configuration using the little 'cog' icon that appears in the upper right corner when you hover over the track:

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And selecting 'Rao et al...' -> 'Configure series' -> 'Flip heatmap' -> 'Yes'

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To yield an upside down view:

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