Error in cyto_gatingTemplate_generate

[Biomiha]

Hi @DillonHammill,

I've tried to use the cyto_gatingTemplate_generate to export a gating template for a GatingSet imported from FlowJo using CytoML (similar use case to Issue #41 ). I get the following error:

 Error in .cpp_getGate(obj@pointer, sampleNames(obj), y) : 
   no gate associated with root node.

If I remove the root node, I lose all nodes so that's not an option. Not sure if anything has changed in how Gating Hierarchies are handled or if the issue is at my end?

Thanks.

[DillonHammill]

@Biomiha, can you send through the output of openCyto::gh_generate_template(gs[[1]]) so I can take a closer look? Looks like cyto_gatingTemplate_generate() is trying to extract the root node as a gate, since this is not stored as a gate, we get the error. I have tried using the function on some test data and it works as expected, I suspect that there is something different about your gating scheme which is causing the error.

[Biomiha]

Thanks @DillonHammill. I'll close this until I've had a chance to see what the issue is.

[Biomiha]

Hi @DillonHammill,

I hope all is well with you. I hope you don't mind if I reopen this issue. I have come across a new error when attempting to generate a gating template from an existing GatingSet that was generated by reading a flowjo workspace into R.

when running:

cyto_gatingTemplate_generate(x = gs, gatingTemplate = "gT.csv")

I get

Error: NA/NaN argument

and when I call .traceback() I get:

[[1]]
stop(gettextf(fmt, ..., domain = domain), domain = NA, call. = FALSE)

[[2]]
stopf(err$message)

[[3]]
.checkTypos(e, names_x)

[[4]]
value[[3L]](cond)

[[5]]
tryCatchOne(expr, names, parentenv, handlers[[1L]])

[[6]]
tryCatchList(expr, classes, parentenv, handlers)

[[7]]
tryCatch(eval(.massagei(isub), x, ienv), error = function(e) {
    if (grepl(":=.*defined for use in j.*only", e$message)) 
        stopf("Operator := detected in i, the first argument inside DT[...], but is only valid in the second argument, j. Most often, this happens when forgetting the first comma (e.g. DT[newvar := 5] instead of DT[ , new_var := 5]). Please double-check the syntax. Run traceback(), and debugger() to get a line number.")
    else .checkTypos(e, names_x)
})

[[8]]
`[.data.table`(gt_entries, 1:ind, )

[[9]]
gt_entries[1:ind, ]

[[10]]
rbind(gt_entries[1:ind, ], gt_bool_chunk[z, ], gt_entries[ind + 
    1:nrow(gt_entries), , drop = TRUE])

[[11]]
FUN(X[[i]], ...)

[[12]]
lapply(seq_len(nrow(gt_bool_chunk)), function(z) {
    gate_pops <- gt_bool_chunk$gating_args[z]
    gate_pops <- unlist(strsplit(gate_pops, "\\||\\&|\\!"))
    gate_pops <- gate_pops[!LAPPLY(gate_pops, ".empty")]
    ind <- LAPPLY(gate_pops, function(pop) {
        match(pop, gt_entries$alias)
    })
    ind <- max(ind)
    gt_entries <<- rbind(gt_entries[1:ind, ], gt_bool_chunk[z, 
        ], gt_entries[ind + 1:nrow(gt_entries), , drop = TRUE])
})

[[13]]
cyto_gatingTemplate_generate.GatingHierarchy(x[[1]], gatingTemplate = gatingTemplate, 
    ...)

[[14]]
cyto_gatingTemplate_generate(x[[1]], gatingTemplate = gatingTemplate, 
    ...)

[[15]]
cyto_gatingTemplate_generate.GatingSet(x = gs, 
    gatingTemplate = "gT.csv")

[[16]]
cyto_gatingTemplate_generate(x = gs, 
    gatingTemplate = "gT.csv")

Seems to be something to do with a call to data.table. Any idea from the traceback about what the issue could be?

Thanks ever so much!