Approaching this question from the other side, is there any alternate format that Excel can produce, which would be more suitable to process?

You may well find that “limited to the Linux environment” is simply not a sustainable technical stricture for this project.   It may well be that, in order to get where you need to go, you have to engage the Windows environment more closely than you now do ... especially if you express a need to edit the graphs.   I think that, at this point, there is a pretty sustainable chance that you simply cannot be successful with your present approach, and if so, you need to make that assessment very soon.