search

alanocallaghan / scater

Clone of the Bioconductor repository for the scater package.
https://bioconductor.org/packages/devel/bioc/html/scater.html
94 stars 40 forks source link

Specifying a Custom Dimension Reduction Name Causes Plotting Error #204

Closed DarioS closed 8 months ago

DarioS commented 8 months ago

Eventually, I want to store UMAP of log-norm counts and also after batch effect correction, so it is necessary to name each one.

example_sce <- mockSCE()
example_sce <- logNormCounts(example_sce)
example_sce <- runPCA(example_sce, name = "PCAlogCounts")
example_sce <- runUMAP(example_sce, dimred = "PCAlogCounts", name = "UMAPlogCounts")
plotUMAP(example_sce, dimred = "UMAPlogCounts") # dimred isn't gracefully accepted.

Error in plotReducedDim(object, ncomponents = ncomponents, dimred = "UMAP",  : 
  formal argument "dimred" matched by multiple actual arguments

... Additional arguments to pass to plotReducedDim.

It should be made clear that ... doesn't accept all of the parameters and why plotReducedDim is needed rather than plotUMAP.