Getting Start

Examples of PhyloVelo and steps are provided in Jupyter Notebook under notebooks folder. For start, please refer to records analyzing simulation, C.elegans and KPTracer datasets.

PhyloVelo on New Dataset

PhyloVelo provides an integrated function for phylogenetic velocity analysis by default whilst specific configurations might need to be adjusted accordingly.

1. import pacakge

import phylovelo as pv

2. import data, filter, normalize and dimensionality reduction

sd = pv.scData(count=xx, phylo_tree=xx)
sd.drop_duplicate_genes()
sd.normalize_filter(min_count=20)
sd.dimensionality_reduction(target='x_normed', method='umap')

3. Run model

depths = [tree.get_depth(sd.phylo_tree.find_any(name=i)) for i in sd.x_normed.index]
pv.velocity_inference(sd, depths, cutoff=0.95, target='x_normed')

4. Porject velocity into embedding and visualization

pv.velocity_embedding(sd, target='x_normed')
fig, ax = plt.subplots()
ax.scatter(sd.Xdr.iloc[:,0], sd.Xdr.iloc[:,1], c=depths, s=100, alpha=0.3)
ax = pv.velocity_plot(sd.Xdr.to_numpy(), sd.velocity_embeded, ax, 'stream', radius=0.8, lw_coef=100, arrowsize=2)

5. PhyloVelo pseudotime analysis

pv.calc_phylo_pseudotime(sd, n_neighbors=100, r_sample=0.8)
fig, ax = plt.subplots(figsize=(8,8))
scatter = ax.scatter(sd.Xdr.iloc[:,0],sd.Xdr.iloc[:,1], c=sd.phylo_pseudotime,cmap='plasma', s=60)
cbaxes = inset_axes(ax, width="3%", height="30%", loc='lower left')
plt.colorbar(scatter, cax=cbaxes, orientation='vertical')

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