More future updates

[LTLA]

Keep this PR open until I've finished refactoring:

• C++ code for calculateQCMetrics
• C++ code for nexprs
• Split plotTSNE, plotPCA and plotDiffusionMap into separate functions.

The rest you'll have to do yourself.

[LTLA]

There are several things that need decisions from @davismcc:

• pca_data_input="fData" got deleted from runPCA, as the output dimensions don't match. It would be more appropriate to write a new function for running PCA on the genes.
• plotTSNESCESet, plotDiffusionMapSCESet and plotPCASCESet are now effectively wrappers around plotReducedDim. A lot of code is repeated here and could be cleaned out.
• We should reduce the number of S4 methods, they're not necessary when the only input is a SingleCellExperiment and there's no need for multiple dispatch.