demo.py

from higashi.Higashi_wrapper import *
config = "/work/magroup/ruochiz/Higashi/config_dir/config_ramani.JSON"
higashi_model = Higashi(config)
higashi_model.process_data()
higashi_model.prep_model()
higashi_model.train_for_embeddings()
higashi_model.train_for_imputation_nbr_0()
higashi_model.impute_no_nbr()
higashi_model.train_for_imputation_with_nbr()
higashi_model.impute_with_nbr()
# Visualize embedding results
cell_embeddings = higashi_model.fetch_cell_embeddings()
print (cell_embeddings.shape)

from umap import UMAP
from sklearn.decomposition import PCA
import seaborn as sns
import matplotlib.pyplot as plt

cell_type = higashi_model.label_info['cell type']
fig = plt.figure(figsize=(14, 5))
ax = plt.subplot(1, 2, 1)
vec = PCA(n_components=2).fit_transform(cell_embeddings)
sns.scatterplot(x=vec[:, 0], y=vec[:, 1], hue=cell_type, ax=ax, s=6, linewidth=0)
handles, labels = ax.get_legend_handles_labels()
labels, handles = zip(*sorted(zip(labels, handles), key=lambda t: t[0]))
ax.legend(handles=handles, labels=labels, bbox_to_anchor=(1.05, 1), loc=2, borderaxespad=0., ncol=1)
ax = plt.subplot(1, 2, 2)
vec = UMAP(n_components=2).fit_transform(cell_embeddings)
sns.scatterplot(x=vec[:, 0], y=vec[:, 1], hue=cell_type, ax=ax, s=6, linewidth=0)
handles, labels = ax.get_legend_handles_labels()
labels, handles = zip(*sorted(zip(labels, handles), key=lambda t: t[0]))
ax.legend(handles=handles, labels=labels, bbox_to_anchor=(1.05, 1), loc=2, borderaxespad=0., ncol=1)
plt.tight_layout()
plt.show()