search

dpeerlab / Harmony

Harmony framework for connecting scRNA-seq data from discrete time points
GNU General Public License v2.0
44 stars 12 forks source link

Unable to reproduce the result shown in the demo notebook #23

Open jzw1999 opened 1 week ago

jzw1999 commented 1 week ago

I recently downloaded the demo Harmony notebook just to see how it worked. I noticed that after running the palantir.plot.plot_palantir_results(), while the pseudotime looked correct the entropy graph looked a little bit off:

image

Essentially the area with the lowest value of pseudotime should agree with the area with the highest entropy (or differentiation potential). However, this is not the case in my run. It seemed that cells with the highest differentiation potential are the primitive endoderm cells at E3.5, not the epiblast cells at E3.5 as shown in the demo notebook.

Also, the imputed expression of FGF4 and GATA6 looked off:

image

Not sure what happened, but the only modification I have done to the notebook is to change the directory of the demo data provided alongside the package, and the force-directed layout did look promising. I would genuinely appreciate any advice on why this notebook produces weird results on my side...

jzw1999 commented 6 days ago

I fixed it myself. After downgrade palantir to 1.3.0 everything makes sense.