messy strings in the UMAP after harmony integration

[chansigit]

I got this result after integrating smart-seq and 10x data of heart cells, can you tell me what parameters could be tuned to avoid this?

before integration

codes:

train_test.harmony = RunHarmony(train_test, c("donor_id", "seq_tech"), plot_convergence = TRUE)

Warning message: “Quick-TRANSfer stage steps exceeded maximum (= 38453600)” Warning message: “Quick-TRANSfer stage steps exceeded maximum (= 38453600)” Warning message: “Quick-TRANSfer stage steps exceeded maximum (= 38453600)” Warning message: “Quick-TRANSfer stage steps exceeded maximum (= 38453600)” Warning message: “Quick-TRANSfer stage steps exceeded maximum (= 38453600)” Warning message: “Quick-TRANSfer stage steps exceeded maximum (= 38453600)” Warning message: “Quick-TRANSfer stage steps exceeded maximum (= 38453600)” Warning message: “Quick-TRANSfer stage steps exceeded maximum (= 38453600)” Warning message: “Quick-TRANSfer stage steps exceeded maximum (= 38453600)” Warning message: “Quick-TRANSfer stage steps exceeded maximum (= 38453600)” Harmony 1/10

Harmony 2/10

Harmony 3/10

Harmony converged after 3 iterations

Warning message: “Invalid name supplied, making object name syntactically valid. New object name is Seurat..ProjectDim.RNA.harmony; see ?make.names for more details on syntax validity”