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FlowSOM Help

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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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CRStevens

Master

Posts: 60

Joined: Thu Jul 17, 2014 5:07 pm

Post Wed Jun 14, 2017 4:29 pm

FlowSOM Help

Rplot01.png
Rplot01.png (6.14 KiB) Viewed 8088 times
Hi All,

I am admittedly a biologist trying to tread water in the new waters of bioinformatics.
I recently have learned some R and wanted to apply that knowledge to test out the FlowSOM package. I seemed to have been able to generate a tSNE and MST, but am really frustrated in now knowing how to fix the legend so it is a column instead of a circle or at least make it larger so it is readable. Also is there a way to make the piecharts to fill the whole node? They are also small and hard to see in this current format. I'm attaching my plot and also below is my PlotStar code:

PlotStars(fSOM, markers = c(31,38,35,36,45,48,53), view="tSNE",backgroundValues = NULL, backgroundColor = function(n) {
grDevices::rainbow(n, alpha = 0.3) }, backgroundLim = NULL, legend = TRUE,
query = NULL, main = "")
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jennifee

Participant

Posts: 1

Joined: Fri May 12, 2017 9:59 pm

Post Wed Jun 14, 2017 7:01 pm

Re: FlowSOM Help

HI there!
I'm also kind of a beginner at R, and only just making the transition from FACS to CyTOF.
In preparing for a first experiment, I've been looking into the R package called cytofkit. It seems like it might be an easier way to make the tsne graphs?
Here is a PLOS paper and a step-by-step tutorial (which includes FlowSOM plots).
http://journals.plos.org/ploscompbiol/a ... bi.1005112
https://www.bioconductor.org/packages/r ... ample.html
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CRStevens

Master

Posts: 60

Joined: Thu Jul 17, 2014 5:07 pm

Post Tue Jun 20, 2017 5:13 pm

Re: FlowSOM Help

Jennifer,

Thank you for the suggestion to use cytofkit! This is truly a great package and allows for simultaneous analysis across many of these analysis algorithms.

As a note I did find a reason for my starplots having such small pie slices and this was due to me now transforming my data prior to building my MST. Once I did this my plots looked much better. As an additional side note they also look very high quality when exported as a PDF.

-Chad
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ErinSimonds

Master

Posts: 50

Joined: Tue May 13, 2014 8:04 pm

Post Mon Nov 06, 2017 5:31 pm

Re: FlowSOM Help

Cytofkit users -- please upgrade to the latest version to fix a critical bug in the clustering. Users that installed cytofkit via Bioconductor between April 2017 and October 2017 are likely to be affected.

Cross-posted from another thread, posted by the cytofkit dev team earlier today:
Thanks for all the recommendations, and glad to see people using cytofkit!

Unfortunately, a bug was identified regarding how clustering was handled in cytofkit, detailed here.

Thankfully, we've fixed the issue and the fix (along with new features) can be accessed by updating cytofkit.
To do so, you can update your version of R to 3.4.2 and update to Bioconductor v3.6 then run the following:

  Code:
source("https://bioconductor.org/biocLite.R")
biocLite("cytofkit")


- Erin

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