I currently use PAGA with the scanpy package (python). In this package we can select one or more trajectories by chosing a specific order of clusters like this:
paths = [('erythrocytes', [16, 12, 7, 13, 18, 6, 5, 10]), ('neutrophils', [16, 0, 4, 2, 14, 19]), ('monocytes', [16, 0, 4, 11, 1, 9, 24])]
and after that specify a root cluster like this:
adata.uns['iroot'] = np.flatnonzero(adata.obs['louvain_anno'] == '16/Stem')[0]
and then compute the pseudotime:
sc.tl.dpt(adata)
I'm sorry but i don't understand how to use root function or milestones in dynverse.
Could someone explain to me how to do this ?
I would like to select three trajectories in PAGA from 10 clusters and then show the heatmap of these trajectories.
Hello everyone,
I currently use PAGA with the scanpy package (python). In this package we can select one or more trajectories by chosing a specific order of clusters like this:
paths = [('erythrocytes', [16, 12, 7, 13, 18, 6, 5, 10]), ('neutrophils', [16, 0, 4, 2, 14, 19]), ('monocytes', [16, 0, 4, 11, 1, 9, 24])]and after that specify a root cluster like this:
adata.uns['iroot'] = np.flatnonzero(adata.obs['louvain_anno'] == '16/Stem')[0]and then compute the pseudotime:
sc.tl.dpt(adata)I'm sorry but i don't understand how to use root function or milestones in dynverse. Could someone explain to me how to do this ?I would like to select three trajectories in PAGA from 10 clusters and then show the heatmap of these trajectories.
Thank you
Nicolas