Martynas,
I've seen that you implemented some error messages, especially concerning GD. However what struck me was the unconditional nature of the error messages. I see them on all pages where a chart is drawn... I guess you need to actually check for errors in PMA_handle_chart_err()
The "Unknown data format." message could be more informative. It now shows up instead of a chart when the number of columns is not 2 or 3. Although I expect the number of supported data format's to increase, it is currently not clear what is used.
One other thing I'm missing is a way back after choosing 'Display chart'. Do you plan to integrate this further with the query result data table?