geographical coordinate assignment and size assignment

Problems with neato when implementing geographical coordinate assignment

Dear all,
I am trying to make a graph to put on the picture of European Map (1600x1200.png). I use neato form a graph
I looked at the coordinates on MS paint. I am aware that, mspaint uses its left top center for 0,0 (pixel) - neato uses its left bottom center for 0,0 (pixel). I modified my code (which forms the dot file) to change the y axis.
I get my graph information from the database and form the dot file by the code.
The problems are:

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