From Array Suite Wiki
Region Plot of Genotype-Phenotype Associations
The RegionPlot GeneticsLand view is a more robust version of LocusZoom and other similar programs that simultaneously plot the p-values of the associations and the Linkage Disequilibrium (LD) in a genome browser context.
To get to this view, you need to first search for an association. From a GeneticsLand instance, type the label that was specified for the result set when it was published to the land in the search box. Select the relevant association type hit from the auto-filled list. Here is an example where the label set during publishing was "hdl":
Search Multiple Associations by choosing the small drop-down arrow next to the search menu. In the Search Multiple Associations menu, users can select Add From Land. This will bring up a menu that can be used to select from all associations in the land.
The default view for association type results is the Association.PValueQQPlot, which will be displayed automatically. To switch to the Region Plot view, use the Select View menu to pick Association Result | Region Plot.
The new view will show a Genome (Manhattan) plot of the top 10,000 results by p-value like this:
There are several ways to select which region to plot. Perhaps the easiest and most direct is to select a peak from the Genome Plot, which will automatically set the region of interest to that area and display the region plot:
This will default to a 500 kb region. To extend the region or get to a specific variant or gene of interest, use the Select Region button highlighted above to open the configuration dialog:
- Maximal region length - extend the region up to 1 Mb
- SNP - current or historical rs ID
- Region - coordinate or region (the center of the region will be used along with the Maximal region length).
- Gene - HGNC] gene symbol (the center of the gene will be used along with the Maximal region length).
These other settings can be changed using the buttons in the same bar as the Select Region button highlighted above:
- Show/Hide Overview - display or hide the Genome plot of the top 1,000 results
- LD Source - select from the different 1000 Genomes Phase 3 continental populations or add a custom source
- LD Measurement - select from r2 (genotypic), haplotypic r2, or D'
- Pairwise LD - display or hide the pairwise LD matrix
While hovering your pointer over the PValue track, use your mouse wheel to zoom in (scroll up) or out (scroll down).
Hover over a data point in the PValue track to display it's p-value or right click on the track and select Show Details to see the table of all p-values.
Select a point in the PValue track (large pink dot) to display the full details table below which includes the calculated LD and all the variant annotations:
Click the little arrow above the details table to hide it.
Use the Search Results tab on the left to highlight points of interest in the PValue track (points that are filtered out remain on the plot but become transparent). Use the View Filtered Table button to see the full table of details for the filtered results only.
In the Task tab on the right are several additional options:
- Reset Region - reset zoom to Maximal region length as configured in Select Region settings.
- Enable/Disable Intro Trimming - Remove or restore intronic regions from plot.
- Hide/Show ToolTip - Hide or display the details of track elements as you hover your pointer over them.
- Organize Tracks - Change the display order of the tracks.
- Change Track Properties - Users can configure the display (label, color, etc) of each track by selecting in the Task Tab menu to modify Track Properties or by right-clicking on the track. One useful feature when visualizing multiple Association Sets is that you can set the y-axis of all tracks to be the same by setting the Auto Scale to False. default the display to be scaled separately for each set so we won't need logic to calculate the uniform scale - the user would need to determine the appropriate top-end of the Y axis
- Save As Image - Export the plot to an image file.
There are several options here for adding more tracks to the plot. See these pages for more details on each.