Save matrix layers

closes #342 (closed)

Applied changes to save the matrix as a layer before it is changed (normalization, batch correction). So our adatas will have three additional layers after core analysis (raw, norm, binarized (ATAC), batch). .X will be a copy of the last created layer. I have also introduced layer parameters to notebooks and functions to use this. It should address the ambiguity discussed in #342 (closed).

closes #352 (closed)

Added a warning during anndata load if adata.raw is detected.