Comments (2)
Hi @caitsimop, the groupNhood
function relies on the Louvain clustering implementation in igraph, which relies on setting a seed.
Following the Bioconductor developer guidelines, set.seed
is never used in any internal code. This should be set by the user before running the function to ensure reproducibility.
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Since R/igraph 1.3 (based on C/igraph 0.9), the Louvain implementation is randomized. This is intentional, and helps users determine whether their results are robust. If the results vary significantly across runs, then there isn't a very well defined community structure in the network, and you should not read too much into the result.
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Related Issues (20)
- plotNhoodGraph doesn't respect factor variables
- MiloR on compositional data HOT 1
- Plotting LFC without filtering by FDR HOT 1
- findNhoodMarkers mixing Gene names HOT 1
- could this packages support TSNE? HOT 2
- When dealing with multiple samples in RDS, should we opt for reduced dimensionality using 'HARMONY' or stick with PCA? HOT 2
- Include batch as a covariate or use batch-corrected latent space for constructing KNN graph HOT 3
- Simple question "Can we add seurat_clusters"? HOT 1
- SpatialFDR after testNhoods() is NA HOT 3
- Problem in buildNhoodGraph on a large dataset HOT 3
- testNhoods() returns :Error in glmFit.default(y, design = design, dispersion = dispersion, offset = offset, : NA dispersions not allowed HOT 5
- Please close this question
- Can I run calcNhoodDistance before countCells HOT 2
- when should buildGraph be used with transposed=TRUE? HOT 4
- findNhoodGroupMarkers: overlapping nhoods in fake.meta HOT 2
- Mixed effects models with contrasts HOT 2
- Choice of fdr.weighting in testNhoods HOT 2
- scVI corrected dimensions with MiloR HOT 1
- plotNhoodSizeHist not lining up with nhoodCounts HOT 2
- Use milo with continuous variable HOT 1
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