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Quick overview plots like Cytobank - R script

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Please be as geeky as possible. Reference, reference, reference.
Also, please note that this is a mixed bag of math-gurus and mathematically challenged, so choose your words wisely :-)
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jimbomahoney

Master

Posts: 73

Joined: Wed Feb 27, 2019 11:21 am

Post Tue May 28, 2019 1:58 pm

Quick overview plots like Cytobank - R script

Hi all,

Since we don't (yet) have a Cytobank licence (and even if/when we do, it will be limited to one machine, which won't be mine!), I wanted a quick way to view all the parameters from a flow (or mass) experiment.

Creating these in FlowJo or FCS Express (we have one licence of each) is obviously time-consuming.

As well as being a beginner to flow & mass, I'm also a beginner with R.

However, I managed to put together the following and figured I'd post it here:

1) As it may be useful / fun for others.
2) For potential feedback on how it could be improved.

One of the things I can't quite get right is the graphical representation.

Anywho, here's the link to the Github page I created for it.

Just like it says there - feedback and suggestions appreciated!
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jimbomahoney

Master

Posts: 73

Joined: Wed Feb 27, 2019 11:21 am

Post Fri May 31, 2019 3:17 pm

Re: Quick overview plots like Cytobank - R script

Lots of improvements added to the latest "release", including a file-> open dialogue and a message box informing how many cell events and what the acquisition rate was (based on the 193 Ir channel).

:D
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jimbomahoney

Master

Posts: 73

Joined: Wed Feb 27, 2019 11:21 am

Post Tue Jun 11, 2019 9:11 am

Re: Quick overview plots like Cytobank - R script

Added events/sec and mean DC as an overlay to each plot.

This helps me get a quick overview of the "quality" of the sample run.
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dtelad11

Master

Posts: 107

Joined: Mon Oct 31, 2016 6:26 pm

Post Fri Sep 27, 2019 5:52 pm

Re: Quick overview plots like Cytobank - R script

I think you might find this helpful:

https://github.com/LKremer/ggpointdensity
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jimbomahoney

Master

Posts: 73

Joined: Wed Feb 27, 2019 11:21 am

Post Mon Sep 30, 2019 7:33 am

Re: Quick overview plots like Cytobank - R script

Thanks El-ad!

I gave it a whirl, but sadly, it's better suited to 2D plots, whereas these time plots are more linear, so the colour scaling doesn't work well.

e.g. stat_density:

Image

e.g. point_density:

Image

I'll bear it in mind for future plotting though!

PS - excuse the typo in the "CD45RA" marker! :D

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