Implements smoothing and parallelisation #12
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jleechung
commented
Jul 25, 2023
jleechung
commented
Aug 29, 2023
| @@ -755,3 +768,8 @@ subsampler = function(knnDF, | |||
| if (sample_renorm) x[, weight := weight / sum(weight), by = from] | |||
| data.table(x) | |||
| } | |||
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For controlling harmonic usage, replace M with compute_agf (and use_agf).
This function converts the boolean flags compute_agf and use_agf to the corresponding M value.
M can still be used in a backward-compatible manner in ComputeBanksy, RunBanksyPCA, RunBanksyUMAP and ClusterBanksy; if it is provided, it overwrites compute_agf (or use_agf). This is documented as advanced usage.
jleechung
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vipulsinghal02
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vipulsinghal02
| } | ||
| if (is.list(bank@own.expr)) { | ||
| # Multiple datasets | ||
| return(bank) |
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I suppose down the road we will also do smoothing for the multi dataset mode?
vipulsinghal02
approved these changes
Sep 25, 2023
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This PR implements label smoothing and parallel clustering.
Other changes include:
sample_size,sample_renorm, andseedfor functionComputeBanksy)Mwithcompute_agfanduse_agfas arguments for specifying which harmonics to computeThis will be the last release / update for BANKSY with BanksyObject. Next release will adopt SingleCellExperiment as a container.