The nodes of the graph (constituent parts of the graph) are also in the graph - there is no difference in this case. (There is nothing 'inside' a graph, just nodes and edges, so there is nothing 'in' could mean, except for those parts.)
"Each graphs" is wrong. After "each" you need the singular.
It should certainly be with the same colour, not by.
I prefer in to of, because the sentence is about what colours are used in the graphs. The nodes are all one colour, and the edges are a different colour, or perhaps the egdes have several different colours.