Obtain feature loadings for pseudo-pca to input on monocle 3 for module analysis?

[EspressoKris]

Hi,

Thanks for the great tool. Conos has been working fantastically on my dataset. I am writing as to ask whether it would be possible to obtain feature loadings for the pseudo-pca computed by Conos. Feature Loadings are required for gene module analysis on Monocle 3, tool that I am currently using to compute lineage trajectories using my Conos embeddings.

Any help would be much appreciated,

Thanks a lot.

[evanbiederstedt]

Hi @kristiangu

Thanks for the issue.

By "feature loadings", I'm guessing you mean something like defined by Seurat?

https://satijalab.org/seurat/v3.0/dim_reduction_vignette.html

2. feature.loadings: stores the weight for each feature along each dimension of the embedding 3. feature.loadings.projected: Seurat typically calculate the dimensional reduction on a subset of genes (for example, high-variance genes), and then project that structure onto the entire dataset (all genes). The results of that projection (calculated with ProjectDim) are stored in this slot. Note that the cell loadings will remain unchanged after projection but there are now feature loadings for all feature

[evanbiederstedt]

Hi @kristiangu

If you give me a few more details with regards to your analysis, I might be able to help out

i.e.

Feature Loadings are required for gene module analysis on Monocle 3, tool that I am currently using to compute lineage trajectories using my Conos embeddings.

what are you precisely doing here? Please show code.

Thanks, Evan

[evanbiederstedt]

Related: https://github.com/cole-trapnell-lab/monocle3/issues/456