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Here are the edits that I made:
0. fixed indentation using cmd+I (sorry, now the whole file looks red!!)
The upload part has same place.
The parameters settings will now appear upon user request on the right-hand side.
The main drawing panel will appear below >> this is so that the plot can take up more space horizontally. Also, this way, the parameters will appear on a separate panel. This still wasn't applied on genome block and snps, but upon approval, I will update them to be consistent with the rest.