The Genetic Map III
The panel of buttons at the top of the genetic map window can be used to manipulate the map in several ways.
Whole, Zoom In, Zoom Out
These buttons on the genetic map (Whole, Zoom In, Zoom Out) control map scale. This is particularly useful for regions of the map containing large numbers of markers. ACeDB will not overlap marker names, and when the map is very crowded, ACeDB will move the names slightly, either horizontally or vertically, to make them fit better. Magnifying the map reduces or eliminates this effect, giving a more accurate view of position and confidence.
The figure seen here does not illustrate the effect of clicking Whole, Zoom In, or Zoom Out, but give them a try. To magnify the map, click in the Zoom In button with the leftmost mouse button. The view will zoom in towards the center of the current map (the center is set using the green sliding bar). Note that Zoom In and Zoom Out affect only the vertical scale of the map. The Zoom Out button reduces the magnification of the map and is used in exactly the same way. Finally, the Whole button instantly returns to the default view of the map, in which all the markers are shown.
GMap Data
The GMap Data button gives an overview of some of the genetic data that underlies the map - specifically, the primary 2-point and multi-point data used to create the unified map. The accompanying figure shows how the button is used. To examine the data "underneath" the map, select a marker (here, tt4) by clicking on it once with the leftmost mouse button. This has the effect of highlighting the marker's name in blue. Next, click the GMap Data button (also with the leftmost mouse button). A series of vertical bars, representing 2-point linkages in this case, appear to the right of the coordinate axis. Clicking once with the leftmost mouse button on one of the bars will highlight the names of the two associated markers. For each marker pair, the distance between the filled boxes at the end of each bar indicates how far apart the markers are on the map.
In some cases, where additional information is known, the GMap Data bars show how closely the primary data matches the unified genetic map. The match is not always perfect since the map is generated using data from many different crosses (and some recombination frequencies have more statistical significance than others). In these cases, there are pairs of open boxes at the ends of the bar. The distance between the centers of the pairs represents the distance between the markers as calculated from the 2-point data. The length of the open boxes is an indication of the error associated with the 2-point distance. You can judge how well the individual 2-point data fits in with the over-all map by seeing how closely the open boxes match the positions of the filled boxes.
The actual data underlying any 2-point pair can be seen by double-clicking (leftmost button) on a bar or its boxes. The information will be presented in a new text window.
You may clear the GMap data from the window by using the pop up window associate with the GMap Data button. Click on GMap Data with the rightmost mouse button and drag down to "Clear Map Data" as shown in the figure. This is especially useful if you have displayed GMap data associated with several loci, and it is no longer possible to see the locus names
On the next page, we discuss the remaining buttons.