Feature/add linkage methods#3
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This commit implements the 'ward' and 'david' (multiple) linkage methods in the `richCluster` package. The 'ward' linkage method is implemented using the generalized formula from Székely and Rizzo (2005), which is suitable for pre-computed distance matrices. The 'david' linkage method is a custom implementation inspired by the DAVID functional annotation tool. It merges clusters based on the number of links between them. The R code has been updated to support these new linkage methods, and tests have been added to `scripts/tests.R`. The README has also been updated to reflect the new features.
This commit implements the DAVID clustering algorithm as a separate function `david_cluster`. The implementation is based on the provided Perl script and includes: - Kappa score calculation for term similarity. - Identification of initial seed groups. - Iterative merging of seeds based on the Dice similarity coefficient. A new C++ class `DavidClustering` has been created to encapsulate the logic, and it is exposed to R through the `david_cluster` function. The README and NAMESPACE files have been updated to reflect these changes, and a test has been added to `scripts/tests.R`.
This commit adds two new visualization functions to the package: `plot_network_graph` and `compare_network_graphs_plotly`. `plot_network_graph` visualizes a single cluster as a network graph, with nodes representing terms and edges representing similarity. Node colors can represent p-values from multiple datasets. `compare_network_graphs_plotly` provides an interactive, side-by-side comparison of network graphs for a single cluster using different p-value types. The necessary dependencies (`igraph`, `fields`, `plotly`, `viridis`) have been added to the `DESCRIPTION` file. Tests and documentation have also been updated.
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