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get a weird figure following the notebook named Bone marrow fates #32
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Are you using ForceAtlas2 algorithm? I think that Some dataset also do not requires diffusion maps as intermediate step and can produce well connected embeddings with clear branch separation with FA2/openTSNE applied directly on PC space. |
Hi!. I try to show the differentiation trajectory of HSC followed the tutorial. After PCA, diffusion, palantir, I got a unexpected figure.
The branch tip cells looks like a string. I try to add the components of PCA as the input of diffusion. I also try to reduce the number of progenitor cells. But Both don't work. Can you give me some advices? Thanks a lot.
pca_projections =pd.DataFrame(adata.obsm["X_pca"],index=adata.obs_names) dm_res = palantir.utils.run_diffusion_maps(pca_projections, n_components=40, knn=30) ms_data = palantir.utils.determine_multiscale_space(dm_res, #n_eigs=4 adata.obsm["X_palantir"]=ms_data.values sc.pp.neighbors(adata,n_neighbors=25,use_rep="X_palantir") adata.obsm["X_pca2d"]=adata.obsm["X_pca"][:,:2] sc.tl.draw_graph(adata,init_pos='X_pca2d') sc.pl.draw_graph(adata,color="celltype")
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