With no Direction Home... Like a Complete Unknown

BioFabric does not like it when the direction home is a complete unknown! (Or something like that; apologies to Bob Dylan).

This posting will be a quick side trip into an undocumented BioFabric feature that can be useful. Whenever you import a SIF file, each link needs to be tagged with a relationship identifier, per the SIF format:

node1_ID [tab] linkTag [tab] node2_ID

BioFabric displays that link tag whenever you mouse over the link, as well as in the Network Magnifier and Network Tour displays. It also insists on knowing whether the relationship indicated by the tag is directed or not. So after a SIF file has been read in, you are confronted with a dialog box that insists that you identify whether each link tag identifies a directed or an undirected edge in the graph. For example, for this tiny little SIF file: 

foo UNDIR bar

foo DIR   baz

You are presented with this dialog box when you import it:

Click on picture to enlarge

In this case, since we wish the link tagged DIR to be directed, we would check the box on the right side of the row labeled  DIR and then hit the OK button to finish the import. When the number of link tags is small, it's not too onerous, and the benefit is that you can create a graph with an explicit mixture of directed and undirected edges.

However, things can start to get painful when the number of link tags starts to grow. The worst case is when you are tagging links with real numbers with a large number of significant digits, since the table in the above dialog will create a row for each one of those values. For that reason, it is best to truncate real-valued link tags to <= 2 digits to keep this from getting out of hand.

If you do have a lot of tags to deal with, you will note there are two buttons on the lower left that give you useful shortcuts. You can make every link either directed or undirected by using those buttons. But what do you do if there is a mixture?

On that count, there is good news and bad news. I'll give the good news first: the Load From File... button allows you to specify the whether link tags represent directed or undirected edges using an input file. Unfortunately, it has not actually been documented anywhere what the file format is... until now! It needs to be an attribute file that has a format similar to the node attribute file used to specify node layout order. The file suffix can be whatever you want, but the file chooser dialog will highlight files with an .rda suffix. (I guess I was thinking that it would stand for relation directed attribute?) The file contents has a required column header line, followed by one and only one row for each and every link tag. Provide true for directed links, and false for directed links.  An example for the given SIF file is:

Relation Directed

UNDIR = false

DIR = true

So, if you load in the above sample file, your SIF import will look like the picture below, with BioFabric using an arrowhead to show the direction of an edge.  But, at the moment, that's all it does to treat directed edges in a special fashion. Most notably, the layout algorithms completely ignore directionality in the current version.

Click on picture to enlarge (but why would you?)

That was the good news. The bad news is that there is a bug in the implementation. If you note, I wrote the two link tags out in all uppercase in this example That's because the Load from File... option is stuck at only recognizing all uppercase tags. If your SIF file is using lower- or mixed-case tags, the program will complain and reject the .rda file. That bug has just been added to the GitHub BioFabric Issues Page! That's the beauty of open source: you got no secrets to conceal (OK, more apologies to Bob Dylan).