search

RGLab / CytoML

A GatingML Interface for Cross Platform Cytometry Data Sharing
GNU Affero General Public License v3.0
30 stars 14 forks source link

flowjo_to_gatingset troubleshoot: "unknown tranformation type!transforms:linear" #147

Open hughmacmillan opened 2 years ago

hughmacmillan commented 2 years ago

Hey friends ... I'm curious how I might work around this issue below. I've loaded xml as a ws, but when I try to get the gating set to tap into data for a few gates in particular, it's objecting to the "tranformation" type that I gather is encoded in the xml? Thanks for any ideas on how to avoid this? The xml is from flow jo 10. Thank you! The issue occurs regardless or the execute and transform settings.

ws <- CytoML::open_flowjo_xml(paste0(folder_here,"/",xml_file_here))

ws

File location: ../data_II/b27/XML.xml

Groups in Workspace Name Num.Samples 1 All Samples 5 2 Patient PBMC 5

gs <- CytoML::flowjo_to_gatingset(ws, name = 1) Error in (function (ws, group_id, subset, execute, path, cytoset, backend_dir, : *: unknown tranformation type!transforms:linear

mikejiang commented 2 years ago

Is the workspace directly exported from flowjo? Shouldn't it be *.wsp file for v10? Can you share example data?

KammannT commented 2 years ago

I get the same error when running the xml file exported from Flowjo using: Power ribbon -> Diagnostics -> "XML for Workspace" -> Copy and paste into R text file -> save as "filename.xml".

However, I receive a different error when running the same code when the original .wsp file is loaded with "open_flowjo_xml(filename.wsp)" instead (see issue #148 )

hughmacmillan commented 2 years ago

Cheers ... indeed I've come to find there's an entire ecosystem of flowjo workspaces and compensations that a partner was attempting to spare me maybe, so i just had xml and naively gave a cytoML a go ... thanks!

H