Sam Morabito comments

Results 88 comments of


                                            Sam Morabito

Question about color of modules in volcano plots

Hi, Can you provide some more details, the code that you ran and the plots that were generated? What is the expected result vs the actual result etc.

Question about color of modules in volcano plots

Looks like a bug to me, each point in the volcano plot should be colored based on the module's color. Can you reproduce this behavior with the tutorial dataset? I...

Error in if (!(multi.group.by %in% names([email protected]))) { : argument is of length zero

Closing issue due to inactivity.

Extracting Co-expression Matrices for Each Condition from hdWGCNA Consensus Network

Hi, At this time, the individual co-expression networks are not saved when you run consensus network analysis. This sounds like it could be an interesting addition, and I can start...

ModuleFeaturePlot - add split.by option

We will work on adding `split.by` as an option for this function in a future update. For now you can just use Seurat's function instead.

Question about exporting the networks to Metascape

Hi, I do not have a way to export to Metascape built in to hdWGCNA. I am not very familiar with Metascape but I will look into it and get...

Question about exporting the networks to Metascape

Hi, I am unfortunately not familiar with Cytoscape (or Metascape). I found this function include in the WGCNA package, maybe you could make use of it. https://rdrr.io/cran/WGCNA/man/exportNetworkToCytoscape.html

Question about module preservation / reproducibility when creating the modules

Currently hdWGCNA does not implement a method for determining the module stability. I am definitely interested in adding this as a new feature but I cannot promise when it will...

Removing anti-correlated genes from module

> some of the genes in my modules aren't moving in the direction I'd like them to I am not really sure what you mean by this statement, can you...

Removing anti-correlated genes from module

If you only want to use genes that increase with time, then you should use that list of genes as the input to hdWGCNA. For example: ``` seurat_obj