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RGLab / flowWorkspace

flowWorkspace
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how to use the open_flowjo_xml #325

Closed lifengt closed 4 years ago

lifengt commented 4 years ago

I am a new person on R, by reading the example from the ?open_flowjo_xml, I got below message, could you please guide me how to read flowjo workspace?

try = "single_gating.xml" real = open_flowjo_xml(try) Error in xpathApply(x, "/Workspace", function(x) xmlGetAttr(x, "version"))[[1]] : subscript out of bounds file.exists(try) [1] TRUE

Thanks! lifeng

gfinak commented 4 years ago

What is "single_gating.xml" ? How did you generate it?

mikejiang commented 4 years ago

Also, make sure you've updated CytoML to the latest release (v2.0.0). From the error message, looks like it was still using the old code base.

lifengt commented 4 years ago

I checked my CytoML, below showed the version: 1.12.1.

Then how should I update the latest version?

Thanks!

Lifeng

packageDescription("CytoML") Package: CytoML Type: Package Title: A GatingML Interface for Cross Platform Cytometry Data Sharing Version: 1.12.1 Date: 2016-04-15

From: Mike Jiang notifications@github.com Sent: Monday, May 11, 2020 11:56 AM To: RGLab/flowWorkspace flowWorkspace@noreply.github.com Cc: Lifeng, Tian lifengt@pennmedicine.upenn.edu; Author author@noreply.github.com Subject: [External] Re: [RGLab/flowWorkspace] how to use the open_flowjo_xml (#325)

Also, make sure you've updated CytoML to the latest release (v2.0.0). From the error message, looks like it was still using the old code base.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/RGLab/flowWorkspace/issues/325#issuecomment-626791434, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIYCZ7J2JYTKR4MSLHEEXSLRRAN2RANCNFSM4M57HOSQ.

lifengt commented 4 years ago

Thanks for your reply.

I open the flowjo workspace, and click the my single gate, and then go to the power, click the Show xml for selected nodes.

Then copy all into a word, and save as a work xml file.

Do you think it is right?

lifeng

From: Greg Finak notifications@github.com Sent: Monday, May 11, 2020 11:54 AM To: RGLab/flowWorkspace flowWorkspace@noreply.github.com Cc: Lifeng, Tian lifengt@pennmedicine.upenn.edu; Author author@noreply.github.com Subject: [External] Re: [RGLab/flowWorkspace] how to use the open_flowjo_xml (#325)

What is "single_gating.xml" ? How did you generate it?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/RGLab/flowWorkspace/issues/325#issuecomment-626790135, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIYCZ7OSIBL7QN4FUECRPPTRRANRZANCNFSM4M57HOSQ.

mikejiang commented 4 years ago

see https://www.bioconductor.org/packages/release/bioc/html/CytoML.html for installation instruction. You need latest R release (4.0).

I suspect you might be only saving a portion of your workspace. Try to find save as from the menu to export the entire workspace as wsp file

gfinak commented 4 years ago

No, it's nonsense. Open the workspace and export the whole thing as XML (for flowJo 9). For flowJo 10, just open the wsp file.

lifengt commented 4 years ago

thanks for all your suggestions.

I think I

Also, make sure you've updated CytoML to the latest release (v2.0.0). From the error message, looks like it was still using the old code base.

Hi,

lifengt commented 4 years ago

see https://www.bioconductor.org/packages/release/bioc/html/CytoML.html for installation instruction. You need latest R release (4.0).

I suspect you might be only saving a portion of your workspace. Try to find save as from the menu to export the entire workspace as wsp file

Thanks!

It fixed the problems, I can read the flowjo files in r now.