Change phat interface so it gives user choice for which file format to output.
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Right now the phat interface outputs three files with each run: _H0, _H1, and _all.csv. The first is the H0 file, second is H1 file, and third has all homology dimensions and the output format that the D3 explorer.html file is expecting. We should probably give users a choice to output just the (_H0, _H1) files, or just the _all.csv file, or both.
The first two file formats, _H0 and _H1, are the standard persistent homology output formats. This format should probably be retained in the app, since this app could be used for multiple purposes. For instance, people might have image data that they want to analyze with the R TDA package, and it is expecting the usual persistence diagram formats.
The other file, _all.csv, will be used for the D3 explorer.html tool.