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Implements smoothing and parallelisation #12
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@@ -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.
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Sounds good.
} | ||
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?
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yes!
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Overall looks good. Let's proceed with the merge.
This PR implements label smoothing and parallel clustering.
Other changes include:
sample_size
,sample_renorm
, andseed
for functionComputeBanksy
)M
withcompute_agf
anduse_agf
as 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.