Problem with RunAzimuth : Error in index$getNNsbyVectorList(query[x,], k, search.k, include.distance) : fv.size() != vector_size

[denizff]

Hi,

First of all, thank you very much for this package. It helps me a lot in my work.

I had a problem recently with RunAzimuth() when I used a reference of my own.
My ref data has 30 PCs. I used the first 13 PCs to run FindNeighbors() and RunUmap()

Then I made a reference with still the first 13 PCs to get the same neighbors :

ref <- AzimuthReference(object = data,
refDR = "pca",
refAssay = "integrated",
refUMAP = "umap",
metadata = "clusters",
dims= 1:13)

After that, I used it with RunAzimuth :

options(Azimuth.map.ndims = 13)
query_projected <- RunAzimuth(query, "path_to_ref", do.adt = FALSE)

and I had the following error :

Error in index$getNNsbyVectorList(query[x,], k, search.k, include.distance) : fv.size() != vector_size

So I checked thourougly the code for RunAzimuth and I found out that the problem was with dims = 13 when I made the reference.
The neighbors were calculated with the first 13 PCs.
But in RunAzimuth code the dims variable takes as a value the length of the refDR which is 30 here :

dims <- as.double(length(slot(reference, "reductions")$refDR))

Because of that, there are errors in FindTransferAnchors and FindNeighbors where dims is set to 30 and not 13 the number of PCs used in the reference for FindNeighbors.

I runned RunAzmituh myself step by step by changing dims variable to 13 instead of 30 and it worked without errors.

I am not sure if it's better to set dims as follow : dims <- as.double(slot(reference, "neighbors")$refdr.annoy.neighbors@alg.info$ndim)
And change the following part :
query[["query_ref.nn"]] <- FindNeighbors(object = Embeddings(reference[["refDR"]][,1:dims],
query = Embeddings(reference[["refDR"]],
return.nghbor = TRUE,
l2.norm = TRUE,
verbose = F )

Best regards,

Deniz Fettahoglu

[denizff]

Sorry, I didn't write the changes correctly to make RunAzimuth work with a reference of my own :

dims <- as.double(slot(reference, "neighbors")$refdr.annoy.neighbors@alg.info$ndim)

query[["query_ref.nn"]] <- FindNeighbors(object = Embeddings(reference[["refDR"]])[,1:dims],
query = Embeddings(query[["integrated_dr"]]),
return.nghbor = TRUE,
l2.norm = TRUE,
verbose = F )

[Gesmira]

Hi, thanks for bringing this up and providing a fix! This is now changed in the seurat5 branch of Azimuth and will be merged into the master branch soon. For details in installing seurat5 packages, see here: https://satijalab.org/seurat/articles/install.html