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visNE plot with phenograph gates

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Posts: 6

Joined: Fri Jan 16, 2015 10:20 pm

Post Fri May 20, 2016 4:44 am

visNE plot with phenograph gates

Hello everybody

Does anybody has experience with phenograph? I am trying to plot the phenograph subsets in a VisNE (like in Levine, 2015 Cell paper). Is there a direct way to do this?

Thank you!



Posts: 17

Joined: Tue Feb 23, 2016 2:18 pm

Post Fri May 20, 2016 12:45 pm

Re: visNE plot with phenograph gates

Hi MarcelaAh

One thing you can do is download the matlab tool that Dana Pe'er lab made publicly available on their website. This allows you to make a ViSNE Graph over which you can apply phenograph clustering.

The way I do it is:

1: In FlowJo, I gate the desired subset and export the FCS of this particular gate.
2: Transform your data if necessary in the matlab implementation (arcsinh 5 for Mass).
3: Subsample
4: Select the parameters for your ViSNE and run the algorithm (right click)
5: after Visne ran, you will see appear two more parameters bh-SNE1 and 2.
6: Select bh-SNE1 and 2, right click and run phenograph. This will add another parameter phenograph. And then you're done.
7: If you export from matlab this sumbsampled FCS, you can use it in FlowJo to make overlays. ie: You may at some point want to display that Visne (linear scale usually from -50 to 50 range for both axes) in a Flowjo Layout and apply phenograph populations by overlaying.




Posts: 113

Joined: Mon Oct 31, 2016 6:26 pm

Post Wed Nov 02, 2016 3:35 pm

Re: visNE plot with phenograph gates

Alternatively, you can reach similar results using R -- all of the required packages are there.

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