flowjo_to_gatingset does not accept data.frame as path about cytoml HOT 5 CLOSED

right, the feature of passing path as a data.frame was deprecated as we re-factored entire parsing code into c++, because it wasn't widely used functionality and we didn't think it was worthwhile to port it.
I have updated documentation to reflect the current state of this parameter.

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Wonderful, thanks for the info and the update.

I have a situation where I need to explicitly define the fcs files, as there are duplicates of the same filename in two folder in the folder structure from the wsp.
Without this functionality, what is the best way to open the wsp? Can I iterate over the fcs files one by one, or would you suggest something else?

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For my purposes, I do iterate over fcs file paths and import them separately as gating sets with CytoML::flowjo_to_gatingset.

When your files (or now gatingsets) are consistent and you want to continue with the gatingset format, you may use flowWorkspace::merge_list_to_gs() to merge a list gatingsets into one gatingset object.

Is it only the filenames that are duplicated or also the meta data of respective FCS files? If it is only the filenames but meta data are unique to each file then you may use the "subset" argument of CytoML::flowjo_to_gatingset to explicitly direct the function to the desired fcs file. The "path" argument may then be the root folder of your fcs files.

There may be a few more details to consider and it may still be a bit tricky though ...

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Thanks for the input, much appreciated. I'll run with your suggestions and figure it out.
As such, no longer an issue. Closing.

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type ?flowjo_to_gatingset and look for section on additional.keys parameter that can be used to address fcs file matching problem

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