Deck 9: Cross-Reference - How This Connects Forward

NumPy's data[rows, columns] indexing corresponds to what pattern in pandas/AnnData?

adata[cells, genes] and df.iloc[rows, cols]

NumPy's .shape corresponds to what in pandas/AnnData?

df.shape and adata.shape

NumPy's np.mean(data, axis=...) corresponds to what in pandas?

df['col'].mean() and groupby aggregations

Plain Python's if cond1 and cond2 corresponds to what in pandas?

df[(cond1) & (cond2)] — note pandas uses &/|, not and/or

The "loop + append" pattern is often replaced by what in pandas?

.apply() or vectorized pandas operations

A Python function like def func(x, default=4) corresponds to what kind of pattern in libraries like scanpy?

Library functions with default arguments, e.g. sc.pp.filter_cells(adata, min_genes=200)

Reading IndexError bottom-up carries over to reading what errors in pandas?

KeyError and ValueError, using the same bottom-up approach