Existing batch after LSI and Harmony

[chen-zhan]

Hi, thanks for providing such an excellent software.
After I run LSI and harmony, I was confussed when I saw the picture which I draw(as the pdf file showed). There are a cluster which is with many batch library.
03.Plot-after-cluster.pdf
I try to follow the 4.2 guidance(https://www.archrproject.com/bookdown/iterative-latent-semantic-indexing-lsi.html), But it seem no use.
` #reducedDims
proj <- addIterativeLSI(
ArchRProj = proj,
useMatrix = "TileMatrix",
name = "pp_IterativeLSI",
iterations = 8, #up
clusterParams = list( #See Seurat::FindClusters
resolution = c(0.1, 0.2, 0.4, 0.4, 0.4, 0.4, 0.4),
sampleCells = 10000,
n.start = 10
),
force = FALSE,
varFeatures = 25000, #down
dimsToUse = 1:30
)

#Remove Batch
proj <- addHarmony(
    ArchRProj = proj,
    reducedDims = "pp_IterativeLSI",
    name = "pp_Harmony",
    force = FALSE,
    lambda = 0.6,
    epsilon.harmony = -Inf,
    corCutOff = 0.7,
    max.iter.harmony = 10,
    groupBy = "Sample"
)`

ArchR-addIterativeLSI-12f6d30188847-Date-2023-02-13_Time-15-56-15.log

I would be very grateful if you have any suggestions on this issue.

[rcorces]

Sorry - I dont provide specific advice for individual analyses on this forum. Your only real option is read the documentation on harmony::HarmonyMatrix to see if there are other parameters or usage tweaks you can use on your particular dataset