seurat v5整合步骤报错处理

参考：https://satijalab.org/seurat/articles/seurat5_integration
有seurat v5中有5种数据整合方法可以选择，其中scVI是需要在同一个conda 环境中新装一个环境的。

• Anchor-based CCA integration (method=CCAIntegration)
• Anchor-based RPCA integration (method=RPCAIntegration)
• Harmony (method=HarmonyIntegration)
• FastMNN (method= FastMNNIntegration)
• scVI (method=scVIIntegration)

obj <- IntegrateLayers(
  object = obj, method = CCAIntegration,
  orig.reduction = "pca", new.reduction = "integrated.cca",
  verbose = FALSE
)
obj <- IntegrateLayers(
  object = obj, method = RPCAIntegration,
  orig.reduction = "pca", new.reduction = "integrated.rpca",
  verbose = FALSE
)
obj <- IntegrateLayers(
  object = obj, method = HarmonyIntegration,
  orig.reduction = "pca", new.reduction = "harmony",
  verbose = FALSE
)
obj <- IntegrateLayers(
  object = obj, method = FastMNNIntegration,
  new.reduction = "integrated.mnn",
  verbose = FALSE
)
obj <- IntegrateLayers(
  object = obj, method = scVIIntegration,
  new.reduction = "integrated.scvi",
  conda_env = "../miniconda3/envs/scvi-env", verbose = FALSE
)

运行的mnn和scvi方法的时候报错：

结果办法就是在运行IntegrateLayers之前，导入SeuratWrappers包即可。
如下：

library(SeuratWrappers)
combined <- IntegrateLayers(
  object = combined, method = FastMNNIntegration,
  new.reduction = "integrated.mnn",
  verbose = FALSE
)
library(SeuratWrappers)
combined <- IntegrateLayers(
  object = combined, method = scVIIntegration,
  new.reduction = "integrated.scvi",
  conda_env = "/miniconda3/envs/scvi-env/", verbose = FALSE
)

注意，每次选一种方法整合即可，还有就是scvi会跑的慢一些。