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RGLab / CytoML

A GatingML Interface for Cross Platform Cytometry Data Sharing
GNU Affero General Public License v3.0
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Export populations as dataframe from a FlowJo workspace #149

Open rohitfarmer opened 1 year ago

rohitfarmer commented 1 year ago

Hi there, I want to export populations as a data frame starting from a FlowJo workspace, and I am stuck after this step:

ws <- open_flowjo_xml("flowjo_workspace.wsp")
gs <- flowjo_to_gatingset(ws, name = 1, path = "all-fcs-files", execute = TRUE)
gate1 <- gs_pop_get_gate(gs, "CD8+")
gate1dat <- gs_pop_get_data(gs, y = "CD8+")

Also, gate1dat seems to be empty. I aim to load a FlowJo workspace, export events/cells per population, and concatenate them in a single file for all the samples. Any suggestions would be helpful. Thanks!

rohitfarmer commented 1 year ago

I figured out this issue. I had to downgrade Bioconductor to 3.13 for the CytoML, flowWorkspace, and flowcore to work. However, now I have a different issue. The exported cells do not match the original data either in the timestamp or the channel values. Somehow, the data is being transformed.

I tried to switch off any transform flag in my functions. However, it is still the same. 

gs <- flowjo_to_gatingset(ws, name = 1, path = file.path(data_folder, "all-fcs-files"), execute = TRUE, transform = FALSE)
getdat <- gs_pop_get_data(gs, y = g, inverse.transform = FALSE)

Any suggestions would be helpful. Thanks!

mikejiang commented 1 year ago

See here https://github.com/RGLab/flowWorkspace/issues/381#issuecomment-1407513245