I am now using PAGA for trajectory inference. And after I use sc.tl.paga() to analysis my scRNASeq data, I tried to plot the cluster. And I found the result plot layout from plot function:1 ) sc.pl.paga(), and 2) sc.pl.paga_compare() are different (but in the tutorial example, they are same).
I compared to the two result plot. There is only embedding difference. I'd like to know are there anyways to make the output plots from these two function looks same (as the tutorial example shows)?