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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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support flowJo_flog in GatingSet2Cytobank #26

Open mikejiang opened 6 years ago

mikejiang commented 6 years ago

On 09/27/2017 09:39 AM, Tyler Burns wrote: Mike,

When I try to run CyTOF data through CytoML, I get the following error, upon running GatingSet2Cytobank():

"Error in export_comp_trans(gs, flowEnv, cytobank.default.scale = cytobank.default.scale, : unsupported trans: flowJo_flog"

I was wondering if you could have a look? I have attached a CyTOF fcs and wsp file (name starts with marrow), a control flow fcs and wsp file that works fine (name starts with flow), and the CytoML-utilizing script I used.

Thanks,

mikejiang commented 6 years ago

The new commit fixed the CyTOF example, here is the import results ( make sure to set cytobank.default.scale = F if you want to preserve the transformation as flog in cytobank , which is similar but not exactly the same as flowJo flog) imageimageimage

but failed on control flow fcs for the notorious unkown error below ,which may need your help to find out the cause. image

tjburns08 commented 6 years ago

This is great! I have confirmed that the import of CyTOF data works on my end. I am currently investigating the "failed to import" error for the flow control.

I have identified another issue while testing your latest version of CytoML. The circle gates rotate (or transpose?) 90 degrees between FlowJo and Cytobank import. Note in the example below that the correct cell-in-gate percentage is preserved in "xml.freq" and "xml.count," but the percentages reported directly in the FlowWorkspace image and Cytobank image reflect that of the rotated gate.

screen shot 2017-11-03 at 12 00 03 pm

Below, I show that this is an issue also in standard flow cytometry data, and I get the same "failed to import" error that you reported. This suggests that this issue exists now for both flow and CyTOF data.

screen shot 2017-11-03 at 12 04 29 pm

Via email, I will send you the files that produced this error, to see if you can replicate this on your end. Please let me know if there is anything else you need for me. Thanks!

mikejiang commented 6 years ago

This ellipsoidGate rotation issue is now fixed. You will need to install the latest cytolib and thenflowWorkspace from github trunk.

tjburns08 commented 6 years ago

@mikejiang I confirm that your fix works on my end. Thank you for your help!

mikejiang commented 6 years ago

@tjburns08 , Can you close it (as well as other issues that are confirmed to be resolved)?