Chromosome Map Scaling¶
Flapjack’s chromosome map (shown above the main graphical genotype area) supports three different display methods. Experiment with the different scaling options to see which ones work best for the data in hand.
Global map scaling¶
Global map scaling simply fits the entire chromosome map onto the screen.
Local map scaling¶
Local map scaling adjusts the chromosome to display only the area covered by the markers currently on screen. Its left visible edge will be the same as the left-most marker’s position, and similarly its right visible edge will be the same as the right-most marker’s position.
As you scroll, the visible region of the map scrolls to accommodate all visible markers, however because the scrolling is based on the fixed-width genotype display, the map will appear to expand and contract as you move.
Classic map scaling¶
Classic map scaling - so called because it was the only scaling method available in early versions of Flapjack - draws a chromosome that is pixel-mapped to the main genotype display, resulting in a visual chromosome that is as wide as the main display. The area of the map visible at any point in time will not necessarily cover the areas holding the markers on screen, so you may see their ‘connecting’ lines disappearing off the left and right edges of the display.