Fixed indentation.
Added ordering of mRNA data for csv output.
Changes to enable reordering and flexibility in metadata in CSV output for mRNA expression data.
Added tests to make sure that clustering was performed and only reorder cols/rows if necessary.
Added function for creating data to download from heatmap matrix.
Updated methyl and miRNA output functions to standardized output mechanism.
Added separate variable for storing the matrix transformed to colors, so the original can be returned.

This has all of the info on clustering order and filtering, so it does not need to be repeated.
Merge pull request #11 from kdaily/PCBC-12

PCBC-12