Flow cytometry data which can be presented in various ways like dot plots, contour, density plots, etc. But in all these representations, the depth of a given population is not very clear in 2D format, which creates a contradiction with the events' distribution and the obtained % value in FlowJo, esp. while visualizing in contour or density plots. I am aware of 3D format representation, in FlowJo version 10.0.7, but unable to find it in version 10.5.3, the one which I am using. It would be great if you can suggest me a way to do that.
Thank you.
Hello Wulligundam,
"FlowJo no longer contains the 3D Viewer platform due to Java 8 compatibility issues"
Quoted from their Release Notes.
http://docs.flowjo.com/d2/getting-acquainted/10-3-release-notes-2/
If you are looking for other visualization methods you can also try FlowJo's tSNE plugin. It is not a 3D solution but a multi dimensional reduction algoritm that slams the multidimensions into a 2D surface plot. http://docs.flowjo.com/d2/plugins/tsne/
Hi Wulligundam,
Unfortunately, that feature has been removed in later versions of FJ. On the Mac, you can install multiple versions of FJ but you need proper Java support to use this feature.
There are several alternatives for you. Firstly, you can export your data as CSV and use other tools to plot them in 3D. Secondly, you can try the non-linear dimension reduction algorithms implemented in FJ that allow output in 2D. FJ implementation of t-SNE is very user-friendly, and the outputs often provide better visualization than 3D cubes or PCA-like projections that were in fashion years ago.
Hi Johan and Anna. Thank you very much for the info. Indeed the t-SNE representation is looking more interesting. Thanks again. :-)
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