different genes

[wbf520qcp]

Hi,
Thanks for developing this awesome tools. I have run it on my data and got fantastic figures. But I wonder how can I retrieve those gene modules so that I can manipulate heat maps with my own code?

Thank you,
Bofei

[joshua-d-campbell]

Hi @wbf520qcp, thanks for trying out our tools! Great question! If you want to get the gene modules, you can use the factorizeMatrix function described here in our tutorial. Briefly, if your celda result is stored in a SingleCellExperiment object called "sce", you can use the following code:

# Factorize the original counts matrix
fm <- factorizeMatrix(sce)

# Get the matrix of module probabilities for each cell
fm$proportions$cell

# Get the matrix of module counts for each cell
fm$counts$cell

Hope that helps. I'm going to convert this to a "Discussion".