About the colors - To achieve a graph-view with multiple clusters I just added all my vaults into a master vault, but now, to facilitate visualization it would be wonderful if we could force different cluster (hence different folder/vaults) to assume different colors (maybe through CSS files for each vault/cluster, that could be seen on the master vault/folder).
About visibility - This would need much more development: the ability to chose which vaults (and correspondent clusters) are seen at any given time, eventually by adding a clickable icon 
near each folder.