## Genetic-map

This display represent the genetic map. You can pick most things.

The contigs are displayed past their last gene -- in many cases they extend much further, but we don't really know how far in genetic units so take our estimate with caution.

If you double click on the contig it interpolates to the physical map using the nearest two genes for which there is genetic map data. Sometimes if the relative order is wrong this can be confusing. All this will improve in the future.

### Menu items:

- Quit: quits the window.
- Help: brings up this help.
- Print: prepares a Post Script file in ./PS which you can then print on your local laser printer.
- Preserve: ensure that the next gmap will be displayed in a different window, otherwise the present one will be reused.
- Recalculate: recomputes the display from the map data. Otherwise, the same display is shown again and again. We could make the recalculation automatic after any update of the clone tress but it would slow the program if you alter some data which do not actually influence the drawing.
- Highlight Selected Objects/Show Selected Objects/Show All Objects: Highlight or restrict to only those objects belonging to the map and the selected keyset (normally the list in the Main Selection Window, or one made by the Query facility). All reverts to the complete unhighlighted map, and removes any highlighting from the GMap Data button option.
- Load/Save Private Map: After editing a map you can save and retrieve it later. The saved map does not appear in the standard chromosome list.

### Buttons

- Whole Chromosome, Zoom In/Out: affect the amount of the map being displayed. They are equivalent to the continuous centering and zooming that you get by picking with the middle button in the left column of the map and dragging up-down to recenter, left-right to zoom.
- GMap Data: Shows CGC map data in graphical form. You can click on the 2point and 3point data entries to see the actual data.
- Highlight/Some/All: Equivalent of the menu entries to highlight or show selected or all objects.
- Drag Gene: Pick a gene or a def-dup, press this button, then drag the gene with the mid mouse button. Useful to edit the map. You can then save your private version.

### Colour Code

When using the "GMap Data" button, colours represent the following information:

- Red: The active object.
- Yellow: Contact to the physical map. Yellow genes are cloned. The little yellow boxes are direct hooks to these clones. The long yellow bar is the contig. Picking it moves you to the corresponding place in the contig.
- Grey: Background to the name of the colored rearrangement.
- Green: Those genes covered by the red rearrangement. Those rearrangements covering a red gene. The gene mapped 2_points relative to the red gene.
- Blue: Those genes not covered by the red rearrangement. Those rearrangements not covering a red gene. The gene mapped 3_points relative to the red gene.
- Magenta : Objects explicitly highlighted with the Highlight option.

The All button removes green, blue and magenta colours.

### Zoom and Recentre

The ZOOM buttons act on the whole map around the center represented by the little green box.

You can recenter the display by pressing with the centre mouse button and dragging, or by picking with the left mouse button and dragging either:

- the small black box sitting on the scale.
- or the long green box at the left of the picture.

to Table of Contents

last edited: July 1994