Predefined Graph Import Still Not Available to Use

[DarioS]

In progress: we are perfecting the functionality to add a precomputed KNN graph (for example constructed with Seurat or scanpy) to the graph slot using the adjacency matrix.

It has been in the vignette for the past three years.

[MikeDMorgan]

Noted, thanks.

[MikeDMorgan]

FYI - it is possible to use a precomputed graph from Seurat, etc, it's just the text that is outdated.

[shaln]

@MikeDMorgan how can I do that? I got the following error when trying to do so using the buildFromAdjacency function. Not quite sure where to begin troubleshooting this, so any help would be greatly appreciated! Thanks.

> all.samples <- readRDS('RDS Files/all.samples.RDS')
> allsamples.sce <- as.SingleCellExperiment(all.samples)
> allsamples.milo <- Milo(allsamples.sce)
> miloR::graph(allsamples.milo) <- miloR::graph(buildFromAdjacency(all.samples@graphs$SCT_snn, k = 20))
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'graph': missing value where TRUE/FALSE needed
In addition: Warning message:
In nrow(x) * ncol(x) : NAs produced by integer overflow

> allsamples.milo
class: Milo 
dim: 24615 48315 
metadata(0):
assays(2): counts logcounts
rownames(24615): AL627309.1 AL669831.5 ... TMEM200C PDYN-AS1
rowData names(0):
colnames(48315): Control_D5_AAACCCAGTAGCGCTC-1 Control_D5_AAACCCAGTCCTACGG-1 ...
  ER_D9_TTTGTTGGTGCTCTCT-1 ER_D9_TTTGTTGTCTATGTGG-1
colData names(26): orig.ident nCount_RNA ... clusters.orig.ident ident
reducedDimNames(2): PCA UMAP
mainExpName: SCT
altExpNames(0):
nhoods dimensions(2): 1 1
nhoodCounts dimensions(2): 1 1
nhoodDistances dimension(1): 0
graph names(0):
nhoodIndex names(1): 0
nhoodExpression dimension(2): 1 1
nhoodReducedDim names(0):
nhoodGraph names(0):
nhoodAdjacency dimension(2): 1 1

[MikeDMorgan]

The error suggests that there may be an issue with the SNN graph from Seurat - can you double check the output from buildFromAdjacency(all.samples@graphs$SCT_snn, k = 20) is a valid Milo object.

[kiwipeel]

Can you please share the codes for seurat objects? I succesfully created milo object from my snn graph but [email protected] is always null. and ı dont know why but spatialfdr values are equeal to NA. But ı got spatialfdr values when ı use directly buildgraph function

[carolienv]

Is it expected that buildFromAdjacency takes up a lot of memory on big datasets?