table(subset_data$stim)
Bac_SEP Control ICU_NoSEP ICU_SEP Int_URO Leuk_UTI URO
3038 15562 4682 4593 9502 11392 9788
subset_data <- subset_data %>% RunHarmony(“stim”, plot_convergence = TRUE)
Harmony 1/10
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 2/10
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony converged after 2 iterations
Warning: 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
Warning messages:
1: Quick-TRANSfer stage steps exceeded maximum (= 2927850)
2: Quick-TRANSfer stage steps exceeded maximum (= 2927850)
harmony_embeddings <- Embeddings(subset_data, ‘harmony’)