Bug (and fix) in LogSeuratCommand when called by Seurat IntegrateData

[jernest1]

When I run Seurat IntegrateData(), the commands slot of the resulting Seurat object contains withCallingHandlers rather than IntegrateData.

require(Seurat)
require(SeuratData)
require(glmGamPoi)

seurat_obj <- LoadData("panc8")
seurat_split_list <- SplitObject(object = seurat_obj, split.by = "tech")
seurat_split_list <- lapply(X = seurat_split_list, FUN = SCTransform, method = "glmGamPoi")

integ_features <- SelectIntegrationFeatures(
  object.list = seurat_split_list,
  nfeatures = 3000
)

seurat_split_list <- PrepSCTIntegration(
  object.list = seurat_split_list,
  anchor.features = integ_features
)

seurat_split_list <- lapply(X = seurat_split_list, FUN = RunPCA, features = integ_features)

integ_anchors <- FindIntegrationAnchors(
  object.list = seurat_split_list,
  reduction = "rpca",
  normalization.method = "SCT",
  dims = 1:30,
  k.anchor = 5, # default = 5, increase to strengthen alignment
  anchor.features = integ_features
)

seurat_integrated <- IntegrateData(
  anchorset = integ_anchors,
  normalization.method = "SCT",
  dims = 1:30
)

names(seurat_integrated@commands)
# [1] "FindIntegrationAnchors" "withCallingHandlers"  

I traced it to an issue in LogSeuratCommand with parsing sys.calls(), line 12 below.

  time.stamp <- Sys.time()
  object <- UpdateSlots(object = object)
  #capture function name
  which.frame <- sys.nframe() - 1
  if (which.frame < 1) {
    stop("'LogSeuratCommand' cannot be called at the top level", call. = FALSE)
  }
  if (as.character(x = sys.calls()[[1]])[1] == "do.call") {
    call.string <- deparse(expr = sys.calls()[[1]])
    command.name <- as.character(x = sys.calls()[[1]])[2]
  } else {
    command.name <- as.character(x = deparse(expr = sys.calls()[[which.frame]])) #THE ISSUE IS HERE
    command.name <- gsub(
      pattern = "\\.Seurat",
      replacement = "",
      x = command.name
    )
    call.string <- command.name
    command.name <- ExtractField(
      string = command.name,
      field = 1,
      delim = "\\("
    )
  }

If I add a second exception for handling IntegrateData, it works normally and returns command information for IntegrateData as I would expect.

  time.stamp <- Sys.time()
  object <- UpdateSlots(object = object)
  #capture function name
  which.frame <- sys.nframe() - 1
  if (which.frame < 1) {
    stop("'LogSeuratCommand' cannot be called at the top level", call. = FALSE)
  }
  if (as.character(x = sys.calls()[[1]])[1] == "do.call") {
    call.string <- deparse(expr = sys.calls()[[1]])
    command.name <- as.character(x = sys.calls()[[1]])[2]
  } else if(as.character(x = sys.calls()[[1]])[1] == "IntegrateData") {
    call.string <- deparse(expr = sys.calls()[[1]])
    command.name <- as.character(x = sys.calls()[[1]])[1]
  } else {
    command.name <- as.character(x = deparse(expr = sys.calls()[[which.frame]]))
    command.name <- gsub(
      pattern = "\\.Seurat",
      replacement = "",
      x = command.name
    )
    call.string <- command.name
    command.name <- ExtractField(
      string = command.name,
      field = 1,
      delim = "\\("
    )
  }

Not sure if that's the most stable or robust solution, but would it be possible to look into the issue and fix it? Happy to submit a PR if you'd like. I'm using the latest versions of Seurat (5.1.0) and SeuratObject (5.0.2). I also saw the issue when I went back to versions 5.0.1 for both packages, and using the standard NormalizeData/ScaleData/FindVariableFeatures approach instead of SCTransform.