View source: R/AntibodyForests_kernels.R
AntibodyForests_kernels | R Documentation |
Performs graph structural comparisons using graph kernel-based method. Currently available kernel methods include: the Weisfeiler-Lehman kernel, the graphlet kernel, and the random walk kernel.
AntibodyForests_kernels( trees, graph.type, kernel.method, additional.param, max.networks )
trees |
(nested) list of AntibodyForests objects, as obtained from the AntibodyForests function, to be compared. |
graph.type |
string - 'tree' will use the usual output of the AntibodyForests function (tree graphs), 'heterogeneous' will use the output of the AntibodyForests_heterogeneous function (bipartite networks for both cells and sequences). |
kernel.method |
string - kernel method to be used, as implemented in the 'graphkernels' R package. 'weisfeiler_lehman' for the Weisfeiler-Lehman kernel, 'graphlet, and 'random_walk'. |
additional.param |
integer - additional kernel options/parameters (e.g., kernel iterations for the Weisfeiler-Lehman kernel). |
max.networks |
integer - maximum number of networks to be compared (will pick the networks with the most number of cells first). |
Heatmap of the graph kernel values.
## Not run: AntibodyForests_kernels(trees, graph.type = 'tree', kernel.method = 'weisfeiler_lehman', additional.params = 10, max.networks = 50) ## End(Not run)
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