Review figures

[hasanbalci]

Some possible improvements I noticed:

• There are many examples where the node labels are not centered.
• Compartment nodes in Figure 2.13 and 2.14 look different from other compartments in the document by their background color.
• In Figure 2.18 and 2.21, negative influence and necessary stimulation edges do not touch to their target nodes.
• In section 2.8.3, a figure that shows the usage of unknown influence edge should be added to make it consistent with other edge types.
• In Figure 2.27, not node doesn't have ports shown with thicker lines.