Perusing the LD Display
The color scheme option (Display menu) allows you to choose among several LD color schemes. The following tables provide details on the color schemes, and a key to the meaning of the currently selected scheme can be dropped down from the "Key" menu in the upper right corner of the screen.
Table 1.1. Standard Color Scheme
D' < 1 D' = 1 LOD < 2 white blue LOD ≥ 2 shades of pink/red bright red
Table 1.2. Confidence Bounds Color Scheme
Strong Evidence of LD dark grey Uninformative light grey Strong Evidence of Recombination white
Table 1.3. r2 Color Scheme
r2 = 0 white 0 < r2 < 1 shades of grey r2 = 1 black
Table 1.4. Alternate D'/LOD Color Scheme
Low D' High D' Low LOD white shades of pink High LOD white black
(r2 and Alt D'/LOD courtesy of Will Fitzhugh)
- In order to help keep the display uncluttered, D prime values of 1.0 are never shown (the box is empty). These values can be switched on or off with the "Show LD values" option in the Display menu.
- The zoom option (Display menu) allows you to select one of three zoom modes. The two zoomed out versions can be useful for browsing large datasets.
- Large datasets also show a "map" in the lower left corner which gives an overview of the D prime display and allows you to navigate quickly. Clicking on an area of the map will cause the main display to jump to that area. This map also shows the currently defined blocks as small black lines across the top.
- Markers with additional notes (as loaded from the info file) are highlighted (the names are green in the zoomed-in view and the lines from the SNP position to the LD chart are green in the zoomed-out view. Details can be viewed by right clicking on the marker number (as mentioned below).
- Right clicking on the marker number (or the equivalent space in the zoomed out views) shows the marker name, minor allele frequency and any additional notes specified in the info file. This can be especially helpful in the zoomed out views which do not display marker names. The last such piece of popup information clicked will be shown at the top of the LD plot. This reminder can be dismissed by left clicking anywhere on the LD plot.
- Right clicking on any pairwise LD comparison will show a more detailed summary of the LD between the two markers in question. This information is also shown at the top of the screen as described above and can be dismissed by left clicking anywhere on the LD plot.
A graph of any variable versus chromosomal location can be added above the LD plot with the "Load Analysis Track" option. Simply create a file with two columns: <position> <value> . Haploview will plot the values in a continuous line along the top of the screen, along with a scale bar on the Y-axis. You can load several analysis tracks which will all be plotted in the same box at the top of the LD plot.
The "Download HapMap info track" option (with an internet connection) allows you to connect to the HapMap Project server and download and display a track with HapMap genotyped SNPs and gene names. If an info file is specified, the default boundaries are the positions of the first and last markers (which is only valid if the info file is in genomic coordinates). You must specify the proper chromosome and genomic build in the dialog box. If you are using a file downloaded from the HapMap website the program will specify the correct default chromosome, build and start/end positions. This track display can be configured with the "HapMap Info Track Options" item in the "Display" menu. Available tracks include HapMap SNPs, Entrez genes, recombination rate, contigs, and GC content.