that is it

I am interested in a specific gene in the module and its most correlated neighbors.
I would like to know if there is a way of getting all adjacent vertices for a particular gene in a module?
I check in the object but the 'fc@coex_network_plot$SLC1A2$data' seems to not contain that information.

Moreover how are defined the degree in that dataframe?
Because when I plot the related network the degrees don't match the number of edge connecting vertices.

Best,
Andy

I am trying to run:

fc <- mod_ora(fc, gmt_in)

Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘mod_ora’ for signature ‘"fcoex"’

It is the same for my and mini_pbmc dataset

Hi, it's me again.

I had successfully ran this a few days ago, but forgot to save the plotted diagrams. It doesn't seem to be working now. I did change computers, but would still like to do some troubleshooting.

The problem is in show_net, although it's possible to have come up earlier since I have loaded a previously-generated fc .RData

show_net(fc)[["TYROBP"]]
Error in check.length(gparname) : 
  'gpar' element 'lwd' must not be length 0

On googling, this seems to have something to do with Pheatmap, ggplot2, or even grid-gpar?

I have re-installing the Pheatmap package manually, it did not solve this issue.

Have you encountered this before? If so, what was the solution?

UPDATE 1:

This is strange, I just tried again on yet another computer, but this time I'm getting a different error:

Error in valid.units(units) : Invalid unit

UPDATE 2:
Went back to the original computer, and it plotted fine. The biggest apparent difference is that this original computer (all parts run) is on Ubuntu, while the other 2 throwing errors are on Windows 10.

Hi again, I was just wondering about intra-cluster modules/networks. The default uses clusters as target, and wouldn't run without this.

I realise the package is already in very late stages of development, and this may be out of scope entirely, so any discussion on alternative ideas would be greatly appreciated.

I don't know the underlying code, so I would assume that the target is essential to the method, and cannot be skipped? In this case, I think maybe supply intra-cluster targets, for example running Louvain again on a subsetted cluster?

Do you think this would be a good idea? Or have any other alternatives I should consider?

They are currently only part of the analysis. They should be a part of the package.

Hi again, I was going through the vignette and found the anti-correlation part, which is quite exciting.

However, it seems to require re-clustering with Seurat.

I checked in fc@adjacency, and there are no negative values (typically used to convey anti-correlation edges).

Are anti-correlations even found at this stage (I think find_cbf_modules)?

Hi Authors, couldn't seem to find any article publication introducing fcoex, and the Readme is rather brief.

Would just like to know what are the novelties or shortcomings addressed by fcoex over CEMiTools? Or any other pros/cons users should be aware of?

Just a quick text summary would be appreciated. Thanks!

Copying a issue sent to me by e-mail:

I want to know which genes correlate with each module-derived cluster (header positive or header negative). How can I do this properly?

Hi, I'm sorry to be bothering again.

I realise you'll probably have these details in your final publication, but I am keen to already be using this tool. I have 2 further questions:

1. I was just wondering how Genes are selected to be the "Names" of each module, is it something like centrality? Or some other metric?

2. Is there any significance in the distance between nodes (length of edges)? I noticed some plots have one tight cluster with surrounding sparse nodes. Or is this purely for aesthetics?

It is a leftover from the adaptation of CEMiTool's code

Copying an issue sent by e-mail.

When running:

save_plots(name = "75percent_10clusters", fc, force = T)

I get the following message:

Some plots have not been defined. Please run the appropriate plot functions. Saving available plots.

$MSGN1

(...)

$DLX3B NULL

$ASPH NULL

[[1]] null device
`

It is not clear to me why the plots are not generated. Restarting R does not help, for example.

I am opening this issue as a notification because fcoex is listed here as a package that relies (depends/imports/suggests) on Seurat. As you may know, we recently released Seurat v5 as a beta in March of this year, with new updates for spatial, multimodal, and massively scalable analysis. For more information on updates and improvements, check out our website https://satijalab.org/seurat/.
We are now preparing to release Seurat v5 to CRAN, and plan to submit it on October 23rd. While we have tried our best to keep things backward-compatible, it is possible that updates to Seurat and SeuratObject might break your existing functionality or tests. We wanted to reach out before the new version is on CRAN, so that there's time to report issues/incompatibilities and prepare you for any changes in your code base that might be necessary.

We apologize for any disruption or inconvenience, but hope that the improvements to Seurat v5 will benefit your users going forward.
To test the upcoming release, you can install Seurat from the seurat5 branch using the instructions available on this page: https://satijalab.org/seurat/articles/install.

Thank you!
Seurat v5 team

current output is weird