Haploview can now take in PLINK outputs. These files require a separate map file or binary map file corresponding to each marker in the output file in order to load. Any output file from PLINK can be loaded provided that it contains a SNP column corresponding to the map file. The map file can contain SNPs that are not present in the associated output file and the SNPs need not be in the same order in the two files. PLINK output is displayed in a single tab containing a sortable table of results and a variety of filtering options below the table. In SNP-based files, you can also load in additional columns using the "Load Additional Results" button.
Filtering options include chromosome and position. The "Filter" dropdown box can be used to further filter on any unrecognized columns in the table. Multiple filters can be applied consecutively by changing the filter options and pressing the "Filter" button. Currently active filters can be viewed using the "View X Active Filters" button where X is the number of currently active filters. This will open a small popup window where filters can be viewed, added, or removed as needed. All filters are jointly applied (logically equivalent to an "AND" operator as opposed to an "OR"). You may search for markers in your data by typing in the “Specify Marker” field and Haploview will search as you type. If you wish to narrow your results to only include markers that match what you have specified, click the “Prune Table” button. You may remove columns from the table by selecting a column from the "Remove Columns:" dropdown menu and using the adjacent "Remove" button. The "Reset" button can be used to revert the table and filters back to their original state (though the sorting state is retained). Please note that non-SNP based files which can be loaded in without a map file do not have the chromosomal or marker filters.
You can use the Fisher method for combining p-values in your PLINK results using the "Combine P-Values" button under the fitering options. This will bring up a dialog that allows you to choose between 2 and 5 p-value columns for use in the Fisher-combined algorithm. Once you click "Go", a new column designated as "P_COMBINED" will appear as the last column in the table. Note that this method does not take into account whether the direction of the effect is the same in multiple samples! Significant associations need to be carefully verified that all associations are in the same direction
You can create graphical plots from your results table using the "Plot" button under the filtering options. Use the Plot Options dialog to specify a title for your plot and various plotting options. At the top of the dialog, select an optional title for your plot. Then choose which columns to use on the X and Y axes of the plot as well as the scale for each using the appropriate drop-down boxes. If you have loaded a SNP based file with an accompanying map file, selecting "Chromosomes" as the X-Axis will plot your results across the chromosomes and will color code them separately. You can also select "Index" for either axis which will simply plot sequential numbers for each result shown in the table for that axis. Additionally, you can specify up to two thresholds for use in the plot, along with which axis to place them on and which direction they should be. Threshold 1 or the "Suggestive" threshold for the -log10 scale will create a blue line and Threshold 2 or the "Significant" threshold for the -log10 scale will create a red line. Datapoints which pass the thresholds will be larger in size then the standard datapoints. Directly beneath the thresholds, you can choose the base datapoint size for results in your plot using the dropdown box. To the right of that, you can use the optional "Color Key" dropdown menu to select a column to be used as a coloring key in the plot. Please note that this functionality will only work when the chosen color key column has 50 or fewer unique values. On the next line, you can use the "Show Gridlines?" checkbox to select whether to show or hide the gridlines in the plot. To the right of that, you can specify the initial width and height of the plot (in pixels). Finally,on the next line you can use the "Export to SVG" checkbox and browse to a location to save your plot to a high quality SVG file. Please note that the SVG option generally takes a great deal of processing power and memory and should only be used when very high quality images are required. In most cases, you can save the plot images as PNG files using the right click context menu described below.
Once the plot has loaded, you can hover over individual data points to see information about that point in a tooltip popup. SNP based data will display the corresponding marker name, chromosome, position, and the value that is being plotted. Non SNP-Based data will either display the corresponding FID and IID values if they are available, or simply the X and Y values for that datapoint. You can also click a datapoint to be taken back to that result in the results table. For many more plotting options including export options, right click anywhere on the plot.
By highlighting a specific result in the table and clicking"Go to Selected Region", you can bring up a dialog to automatically fetch that region from the HapMap website and load it into Haploview. The dialog allows you to specify the size of the region and the HapMap analysis panel that you wish to download. It will also allow you to search in the surrounding area for known SNPs and Genes. This information is obtained from the Genecruiser service (http://genecruiser.broad.mit.edu/), and includes common information on found SNPs and Genes. You may optionally choose to define your HapMap download to center on a loci found by the search. You can also optionally choose to annotate the columns from the PLINK tab to annotate in the LD Plot. Once the region has been successfully loaded into Haploview, the initially selected marker will be highlighted in blue on the Check Marker and PLINK tabs. SNPs that appear in the PLINK tab are now marked in green on the LD Plot, and the specific result that you specified is further highlighted in white. You can view the annotated data from the PLINK table by right clicking on the marker number in the LD Plot. You can use the "Force in PLINK SNPs" button in the Tagger panel to force include all the SNPs contained in the PLINK results tab. Please note that using "Go to Selected Region" requires an active internet connection.
The "Export Tab to Text" option in the File menu will export a text file containing the current view of the results table. This file will preserve any sorting and filtering that you've enabled in the table.