Error: 'do_ExpressionHeatmap' is not an exported object from 'namespace:SCpubr' about scpubr HOT 3 CLOSED

Hi @kaizen89,

Thanks for using my package!

Regarding SCpubr::do_EnrichmentHeatmap() with flavor = "UCell", the requirement of having R v4.2.0 is set by the UCell developers and I have no saying on that. I hope you understand.

The function SCpubr::do_ExpressionHeatmap() is still an in-development function that will be added in the next CRAN update. If you still want to use it, make sure that you have updated SCpubr to the latest commit. The error log that you have there stems from the fact that the function is not exported in your current version-commit of the development package. You can access the function via the last commit:

devtools::install_github("enblacar/SCpubr", ref = "41d1fb451fd17e0a55a2d4881f8d315b516841c7")

However, since you are using the development version outside the specific releases pinned here, errors are to be expected.

Having all this said, this function is designed to work with genes only (more precisely, with the features of the provided assay), as the idea of it is to see the expression on a common color scale. So far I did not anticipate people trying to use it with other metadata variables, but this is something I will probably restrict via a specific error message before update v1.1.0, as otherwise you might include a gene than ranges expression from 0 to 1 and the include the UMI column that might bring the scale from 0 to 8000.

If you still want to use the UCell scorings that you seem to have already computed in the object, I'd suggest creating a specific assay with them:

# Retrieve your scores.
scores <- sample@meta.data[, paste0(names(top50_signature),"_UCell_sig")]

# Turn it into a matrix (scorings become the features, cells remain as cells).
scores <- t(as.matrix(scores))

# Create an assay object.
scores_assay <- Seurat::CreateAssayObject(counts = scores)

# Add it to your Seurat object.
sample@assays$UCell_scoring <- scores_assay

# Plot the features.
p <- SCpubr::do_ExpressionHeatmap(sample = sample, 
                                  features = paste0(names(top50_signature),"_UCell_sig"), 
                                  assay = "UCell_scoring")
p

That should do the trick for you!

Best,
Enrique

from scpubr.

Hi @kaizen89,

SCpubr version 1.1.0 is already on CRAN!

Please consider updating to get all the new functionalities:

install.packages("SCpubr")

Thanks again for using the package!
Enrique

from scpubr.

Thanks for your prompt response

from scpubr.