fastMNN error when supplying SCE with dimnames and non-NULL use.dimred

[PeteHaitch]

suppressPackageStartupMessages(library(batchelor))

B1 <- matrix(rnorm(10000), ncol = 40, dimnames = list(NULL, paste0("B1_", 1:40)))
B2 <- matrix(rnorm(10000), ncol = 40, dimnames = list(NULL, paste0("B2_", 1:40)))
batch <- c(rep(1, ncol(B1)), rep(2, ncol(B2)))
sce <- SingleCellExperiment(list(logcounts = cbind(B1, B2)))
assay(sce, "cosnormed") <- cosineNorm(logcounts(sce))
set.seed(666)
pcs <- multiBatchPCA(sce, batch = batch, assay.type = "cosnormed")
#> Warning in sweep(centered, 2, w, "/", check.margin = FALSE): 'check.margin' is ignored when 'x' is a DelayedArray object or
#>   derivative
reducedDim(sce, "PCA") <- do.call(rbind, pcs)

set.seed(666)
named_sce <- fastMNN(sce, batch = batch) # Works
#> Warning in sweep(centered, 2, w, "/", check.margin = FALSE): 'check.margin' is ignored when 'x' is a DelayedArray object or
#>   derivative
set.seed(666)
unnamed_sce <- fastMNN(unname(sce), batch = batch) # Works
#> Warning in sweep(centered, 2, w, "/", check.margin = FALSE): 'check.margin' is ignored when 'x' is a DelayedArray object or
#>   derivative
all.equal(reducedDim(named_sce), reducedDim(unnamed_sce), 
          check.attributes = FALSE) # Sanity check
#> [1] TRUE

unnamed_pca <- fastMNN(unname(sce), batch = batch, use.dimred = "PCA") # Works
all.equal(unnamed_pca$corrected, reducedDim(unnamed_sce)) # Sanity check
#> [1] TRUE
named_pca <- fastMNN(sce, batch = batch, use.dimred = "PCA") # Errors
#> Error in dimnames(x) <- dn: length of 'dimnames' [2] not equal to array extent

^{Created on 2019-05-22 by the reprex package (v0.2.1)}

Session info

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The last line should work and all.equal(named_pca$corrected, reducedDim(named_sce) should be TRUE, right?
I got a bit lost in the traceback() trying to figure this one out.

[LTLA]

It's a recurring nightmare with the name handling. At some point, I was using withDimnames=FALSE in a misguided attempt to squeeze out some more efficiency. But this causes no end of problems when you try to add the names back in, because the diversity of sources (in SCE assays, in SCE reducedDims, as a raw matrix of expression values, as a matrix of PCs) makes it difficult to re-extract the names. In this case, the names were not properly extracted from the SCE reducedDims, hence the observed error.

The easiest solution is just for me to go in and remove withDimnames=FALSE, but the names are being lost somewhere else along the line. You can try to find it but otherwise I will deal with it tomorrow.

[PeteHaitch]

I'm all too familiar with that nightmare.
Would you mind porting the fix to the release branch if the change is small enough?

[LTLA]

Fixed in 1.1.2 and 1.0.1.

[PeteHaitch]

Thanks, Aaron!