search

HelenaLC / CATALYST

Cytometry dATa anALYsis Tools
66 stars 30 forks source link

CATALYST::pbMDS produced plots with cluster cells clumped together on 1 side? #350

Closed denvercal1234GitHub closed 1 year ago

denvercal1234GitHub commented 1 year ago

Hi there,

Thanks for the package.

I performed the clustering and visualise using the code below, but as you can see the clusters are clumped together on 1 side at 0 for MDS dim.1 Is this a technical error?

Thank you for your help. 

CATALYST::pbMDS(F37_channelCD3CD8_fcs_data_sce, shape_by = "manualInspect_strangeFCS", size_by = T, k="meta25", by="both")
Screenshot 2023-06-21 at 16 06 05 Screenshot 2023-06-21 at 16 06 28
HelenaLC commented 1 year ago

I cannot answer this question, and it doesn't look like an issue on CATALYSTs end. Basically there is one outlier (sample ?, cluster 9, can't tell the shape...), which causes all other points to appear "squeezed" along the 1st MDS dimension. But what's causing this / what's off with those cells requires investigation...

Issues posted on GH are meant for software-related inquiries, bug reports, potential feature requests etc., and I reserve (my free) time to lend users support as best is possible. However, for help interpreting the data I suggest other platforms, or consulting with a colleague / bioinformatician, or similar.