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nolanlab / vortex

VorteX Clustering Environment - Java graphical tool for single-cell analysis, clustering and visualization. Latest release:
https://github.com/nolanlab/vortex/releases
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Graph not opening #20

Open albertapaul opened 5 years ago

albertapaul commented 5 years ago

Hi,

I was able to successfully imported spectral flow data (New Cytek Aurora platform) of human PBMCs cultured for 7 days with different antigens. These were imported after FCS express gating on memory CD4 T cells. Some background: Cells labeled with CellTrace violet and staining with 9 cytokines, 2 activation markers and 4 subset markers. Point to see is if different variant antigens induce different phenotypes, then compared different subjects. Clustering worked and PCA graph of optimal elbow value selected clusters loads, after quick inspection the properties of the clusters looks similar to conclusions after data-analysis bi-exponential gating Only I cannot get any other graphs, I get the message at least 2 clusters must be selected. Where do I select them, I tried selecting in the upper right window of cluster characteristics and heat-map. Also how can I do cluster analysis of the individual files? I imported several with the option to analyze later individually, as I understood this is possible, checked. Hope this works for me as biexponential gating and tSNE (Visne) does not pick up <1% populations. Thank you. Alberta.

albertapaul commented 5 years ago

I mean Visne does not pick up small populations

nsamusik commented 5 years ago

Hi Alberta,

Happy to hear you had some success with clustering spectral data!

In order to select clusters, just press anywhere in the cluster heamap and then press Ctrl+A (or Apple+A on Mac). You should be able to see rows being selected in the table as their background will turn blue. If the problem persists try restarting VorteX.

Thanks!

Nikolay

On Wed, Oct 31, 2018 at 4:12 PM albertapaul notifications@github.com wrote:

I mean Visne does not pick up small populations

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albertapaul commented 5 years ago

Hi Nikolay,

Yep that works, thank you.

Different question:

How to plot graph of the different FCS files (stimulation conditions)?

I selected the option for a "special annotation object" but do not see this option when plotting?

I am sure I might have to "bug" you more.

Thank you so much for your help.

Alberta (aka Liesbeth)

Alberta G.A. Paul, Ph.D., Research Scientist, University of Virginia, Department of Medicine, Division of Asthma, Allergy & Immunology P.O. Box 801355 MR4, Room 5061 Tel.: 434-924-1114 Fax.: 434-924-5779

From: Nikolay Samusik notifications@github.com Sent: Thursday, November 1, 2018 1:38:00 AM To: nolanlab/vortex Cc: Paul, Alberta Gerarda (ap8n); Author Subject: Re: [nolanlab/vortex] Graph not opening (#20)

Hi Alberta,

Happy to hear you had some success with clustering spectral data!

In order to select clusters, just press anywhere in the cluster heamap and then press Ctrl+A (or Apple+A on Mac). You should be able to see rows being selected in the table as their background will turn blue. If the problem persists try restarting VorteX.

Thanks!

Nikolay

On Wed, Oct 31, 2018 at 4:12 PM albertapaul notifications@github.com wrote:

I mean Visne does not pick up small populations

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/nolanlab/vortex/issues/20#issuecomment-434878760, or mute the thread https://github.com/notifications/unsubscribe-auth/ADacL4pqez8ZXN581rPfwdYjpvAc4ADuks5uqi5IgaJpZM4YFg8I .

-- Nikolay

This message is intended for the named addressee(s) only. It may contain

privileged and confidential information and protected by a copyright. Any disclosure, copying or distribution of this message is prohibited and may be unlawful. If you are not the intended recipient, please destroy this message and notify me immediately. Thank you for your cooperation.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/nolanlab/vortex/issues/20#issuecomment-434936349, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AqllFWoHdhFdC25_4B9bhBEWpv6DNd0Rks5uqoi4gaJpZM4YFg8I.