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In Grapher, the first two columns of data are automatically used for the X and Y values.  If the data contains recognized date formats, the axes are automatically formatted for date labels.  Even if you change the X and Y columns, the formatting remains on the axes. If you do not want the date labels, you can change them to show regular numbers for the tick labels.  To do so, follow these steps:

1. Click once on the axis to select it. 
2. In the property inspector, open the Tick Labels tab. 
3. Open the Major label text section. 
4. Uncheck the Use date/time format option. 

The axis will now use regular numbers for the tick labels.