MapViewer
CarrotOmics strives to have all published linkage maps for carrot available in the database. The maps are visualized using MapViewer.
MapViewer is a tool for viewing and comparing genetic maps using the Tripal MapViewer module version 2. Tripal MapViewer is a modern replacement for the cmap program which has not been updated since 2009.
The MapViewer Quick Start can be accessed from the Tools menu in the header, and on this page there are links to example maps and correspondence matrices. Maps can also be reached from the Map Search under the Search menu. Alternatively, from the Marker Search page, selected markers will display a link to any linkage map that they are present in. The Map Overview pages for each of the maps display summary graphics of all linkage groups, and clicking on a linkage group opens a more detailed view in MapViewer.
MapViewer displays the complete linkage group on the left, and the selected region on the right. The selected region can be changed by dragging and resizing a window on the complete linkage group on the left side. There is a legend of the marker colors below the linkage group figure. Information about the markers is displayed in the upper right corner when the pointer is over a marker name on the right side graph. Clicking on the marker name on the rights side graph, opens the marker details page.
A different map or linkage group can be displayed using the controls at the bottom of the MapViewer page. The color of the markers and which markers are displayed can be changed with the controls. The ruler and marker positions can also be toggled on or off. After changing any of the four parameter sections, the Submit button must be pressed to display the changes.
Pictures from MapViewer
MapViewer allows users to export figures as a high-resolution PNG file that is suitable for publication. Items that can exported have a clickable camera icon that will trigger a file download. Users can export the map overview which has all the linkage groups (Fig. 1), a single linkage group (Fig. 2), a linkage group comparison (Fig. 3), a dot plot (Fig. 4) or a correspondence matrix (Fig. 5).
Figure 1. How to download a map overview.
Figure 2. How to download a linkage group figure.
Figure 3. How to download a linkage group comparison figure.
Figure 4. How to download a linkage group comparison dot plot.
Figure 5. How to download a linkage group comparison correspondence matrix.