Update run_magic_imputation to make setting small values to 0 optional

[jordanc17]

These changes keep the default behavior of run_magic_imputation the same while allowing users to select if the matrix will be made sparse and the threshold that will be used to set small values to zero.

[katosh]

Thank you @jordanc17! This change makes the clipping optional without breaking old behavior.

I made some additions in b0f949e to make the matrix a proper sparse matrix. This additional change breaks old behavior in the case when a dense X is supplied and sparse=True. While the values are the same it now converts the resulting sparse matrix into a sparse format. @ManuSetty