Question about visualizing topologies after projection in module preservation analysis

[jmkotah]

Hello hdWGCNA team!

First of all, thank you for this great package. I wanted to ask a quick question about visualizations after doing module preservation analysis. The gist is that I split my dataset into cells from diseased and control samples, and am trying to check if modules observed in controls are preserved in diseased samples, and vice versa.

In line with the discussion in #393, I made two subset datasets, and in each I ran the standard hdWGCNA pipeline. I was then able to check module preservation with the NetRep approach in the vignette, and have gotten summary statistics and the lollipop plots to work as well.

My question is similar to what was asked in #358, namely that I am having problems visualizing topologies and connectivity after the preservation analysis. For instance, I get an error when running ModuleTopologyHeatmap, due to the projected hdWGCNA experiment not having any associated connectivity (and thus a failure in the GetDegrees part of the code).

In the vignette the projection was done first, after which the 'usual' hdWGCNA was performed. In my case I already have a pre-analyzed network and TOM available, but of course the projected hdWGCNA experiment still does not have any network information. In both examples it seems to me that the projected hdWGCNA experiment itself also does not have connectivity, but that it's relying on the TOM from the other experiment.

I'm wondering, as in #358 (comment), whether the idea would be to process the projected experiment to get connectivity metrics (check soft powers, construct network, etc), but would that not in principle overwrite the projected modules that were found? I would be grateful for any recommendation you might have.

In any case, thanks again for this very helpful package!

[MujeebQadiri]

Hi, I am facing a similar situation were you able to get around this issue?

[jmkotah]

Hi, unfortunately I have not. Hopefully we can get some advice about the topology at some point from the hdWGCNA team. I have mostly just been trying to interpret the preservation of modules between conditions based on the statistics (although some of the metrics are not entirely clear to me).

[smorabit]

Hi,

Thank you all for writing about this issue. I understand that there is some confusion about visualizing the topologies of different networks, and how it relates to module preservation analysis. I have been working on revising the tutorial to better clarify this and to avoid further confusion. However, it won't be ready for a few weeks due to summer vacations etc.