MiNAA v1.1.0

[reednel]

MiNAA v1.1.0

Overview

This update brings a large number of peripheral changes to MiNAA which enhance user experience and understanding, code readability, and the ability to interface with other programs. Core functionality has not changed at all. Any commands and inputs previously run on version 1.0.1 will work and output the same results.

Feature: Webapp Adaptation [PR]

The bulk of the functional changes in this update are the addition of arguments for interfacing with the R Shiny app (in development). In addition, slight refactoring was made across file_io.cpp, making naming conventions more uniform and select functions a bit more generic.

New Arguments:

-Galias=: an alias for the G file.
-Halias=: an alias for the H file.
-Balias=: an alias for the B file.
-p: passthrough; whether or not to write the input files into the output folder.
-t: timestamp; the output folder's name includes the date and time of execution.
-g: greekstamp; the output folder's name includes the values for alpha and beta.

Feature: Biological Similarity Conversion [PR]

The new optional argument enables the user to input a biological similarity matrix if that's more convenient. Previously the bioligical input was required to be a cost matrix.

New Argument:

-s: similarity conversion; for each entry in the given biological matrix, the value (post normalization) is replaced with 1 - value. 

Feature: Similarity Threshold [PR]

For computational complexity reasons, our alignment algorithm finds a complete (rather than partial) matching between two networks. This means that certain nodes may be matched by the algorithm, even if they obviously bear no relation (have a very low similarity). Hence, the value of the argument added below. This is completely optional, and the default value of 0 keeps the same logic that existed previously.

New Argument

-st=: similarity threshold; define a value in range [0, 1] above which aligned pairs are included in the output.

The other notable addition (and source of bloat) on this PR is the rewrite to the examples. All have been pulled out of the root README in favor of deeper explanation with actual inputs (using real-world data) and outputs in the example/ folder. The previous single example in that folder has been removed, as it was essentially a duplicate of one single network pair from the Simulation data. This has no impact on functionality.

Additional Changes

No additional functional changes were made, just cosmetic updates causing more diff bloat.

• All source and header files were autoformatted, making substanceless updates to 11 files and hundreds of lines.
• example/ was renamed to examples/, reindexing 25 files and thousands of lines.
• License was updated for 2024, and the spelling was made uniform.