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| I delete the map in the plot window and the map is removed, but the axes are still there. Why? |
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If you click on a map in the plot window in Surfer 9, you will most likely select the map layer and not the map frame. You can see this in the Object Manager. The map layer is the map type, ie. Contours, and the map frame is the entire map (called Map by default). If you only have the map layer selected, when you press Delete you will then remove the map layer only leaving the empty map frame (the axes) still visible on the screen.
To delete an entire map in Surfer 9, select Map from the Object Manager and press Delete on the keyboard (or right click over Map and go to Delete).
This has been changed in Surfer 10. In Surfer 10, if you select and delete the only map layer in a map, the map frame will also be deleted.
See also: What is a "map frame" or a "map layer"
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