-
Notifications
You must be signed in to change notification settings - Fork 29
API Reference
Jean-Daniel Fekete edited this page Aug 26, 2015
·
21 revisions
Wiki ▸ API Reference
Everything in Reorder.js is scoped under the reorder namespace.
Reorder.js uses semantic versioning. You can find the current version of Reorder.js as reorder.version.
See one of:
- Core - Matrix, Graphs, Permutations
- Conversion - Converting Matrix into Graphs and vice versa
- Reordering - Finding a good order
- Measure - Quality measures
- Visualization - Visualizing the results
- Statistics/Linear Algrebra - Linear Algebra
- reorder.condition - scale the rows of a matrix to be in [0,1].
- reorder.random_matrix - generate a random matrix of size (n,m).
- reorder.transpose - transpose a matrix (swap rows/columns).
- reorder.graph - create a graph object.
- graph.nodes - get or set the array of nodes.
- graph.node_indices - return the list of node indices.
- graph.generate_nodes - fills the graph with n nodes.
- graph.links - get or set the array of links between nodes.
- graph.link_indices - return the list of node indices.
- graph.link_distance - get or set the link distance.
- graph.directed - get or set whether the graph is directed or not.
- graph.init - initialize the graph structure.
- graph.edges - return the edges connected to a node.
- graph.inEdges - return the incoming edges of a node in a directed graph.
- graph.outEdges - return the outgoing edges of a node in a directed graph.
- graph.degree - return the degree (number of edges) of a node.
- graph.inDegree - return the number of incoming edges of a node in a directed graph.
- graph.outDegree - return the number of outgoing edges of a node in a directed graph.
- graph.sinks - return the nodes with no outgoing edges in a directed graph.
- graph.sources - return the nodes with no incoming edges in a directed graph.
- graph.distance - return the distance of a link.
- graph.neighbors - return the list of nodes with an edge to the specified node.
- graph.other - return the other endpoint of an edge, given a link and an edge.
- graph.components - return the list of connected components of the graph.
- reorder.graph_random_erdos_renyi - return a random graph.
- reorder.graph_empty - return a graph with a specified number of nodes and no links.
- reorder.graph_random - return a random graph with a specified size.
- reorder.graph_complete - return a complete graph with a specified size.
- reorder.graph_connect - connect all the components of a specified graph.
- reorder.all_pairs_distance - return the distance matrix of the weighted graph.
- reorder.bfs - apply a function over the nodes of a graph in Breadth-First order.
- reorder.bfs_distances - compute the Breadth-First distances from a node of a graph.
- reorder.all_pairs_distance_bfs - compute the distance between all nodes of a graph using the Breadth-First-Search algorithm.
- reorder.permutation - return a identity permutation of a specified length.
-
reorder.inverse_permutation - return the inverse of a permutation so that
inverse_permutation(permutation(i)) == i. - reorder.permute - apply a permutation to a list/vector.
- reorder.permute_inplace - permutes a list/vector in place.
- reorder.permute_transpose - permutes the columns of an array.
- reorder.randomPermutation - return a random permutation of a specified length.
- reorder.stable_permute - apply a permutation that starts with the lowest index of the two ends.
- reorder.mat2graph - transform a matrix into a graph.
- reorder.graph2mat - return a matrix from a graph.
- reorder.graph2valuemats - return a valued matrix from a weighted graph.
- reorder.valuemats_reorder - reorder an undirected graph using its value matrix and a matrix ordering algorithm.
- reorder.barycenter_order - reorder a graph using the barycenter heuristic.
- reorder.adjacent_exchanges - improves a barycenter_order by swapping adjacent vertices when that decreases the number of crossings.
- reorder.bfs_order - reorder an undirected graph using a Breadth-First order.
- reorder.cuthill_mckee_order - reorder an undirected graph using the Cuthill-McKee bandwith reduction algorithm (bad).
- reorder.reverse_cuthill_mckee - reorder an undirected graph using the Reverse Cuthill-McKee bandwith reduction algorithm (bad).
- reorder.optimal_leaf_order - reorder a table using the Optimal Leaf Ordering algorithm.
- optimal_leaf_order.distance - get or set the distance function for the optimal leaf ordering algorithm.
- optimal_leaf_order.linkage - get or set the linkage for the hierarchical clustering used by the optimal leaf ordering algorithm.
- optimal_leaf_order.distance_matrix - get of set the distance matrix used for computing the optimal leaf order.
- reorder.order - Manipulation and control of optimal leaf ordering parameters to interact with the reordering.
- order.distance - get or set the distance function for the optimal leaf ordering.
- order.linkage - get or set the linkage for the hierarchical clustering used by the optimal leaf ordering algorithm.
- order.limits - get or set the min/max indices of the matrix manipulated.
- order.except - get or set ranges of indices the ordering algorithm should not change.
- reorder.pca_order - reorder a matrix using PCA.
- reorder.sort_order - reorder a matrix according to a sort function.
- reorder.spectral_order - reorder a graph according to its Fiedler vector.
- reorder.bandwidth - compute the bandwidth of an ordered graph.
- reorder.edgesum - compute the edge sum measure of an ordered graph.
- reorder.count_crossings - compute the number of crossing of a 2-layer graph.
- reorder.fiedler_vector - compute the Fiedler vector of a graph: the eigenvector with the smallest non-null eigenvalue of the Laplacian of the graph.
- reorder.correlation - compute the Pearson correlation of two rows.
- reorder.covariance - compute the covariance of two rows.
- reorder.covariancetranspose - compute the covariance of two columns.
- reorder.distance - provide several distance functions.
- distance.euclidean - Euclidean (L2) distance.
- distance.manhattan - Manhattan (L1) distance.
- distance.minkowski - Minkowski distance.
- distance.chebyshev - Chebyshev distance.
- distance.hamming - Hamming distance.
- distance.jaccard - Jaccard distance.
- distance.braycurtis - Braycurtis distance.
- reorder.dist - compute pairwise distances.
- reorder.distmax - compute the maximum distance in a distance matrix.
- reorder.distmin - compute the minimum distance in a distance matrix.
- reorder.dist_remove - remove a line/column from a distance matrix.
- reorder.hcluster - hierarchical clustering.
- hcluster.linkage - get or set the type of linkage.
- hcluster.distance - get or set the distance function.
- hcluster.distanceMatrix - get or set the distance matrix.
- reorder.laplacian - compute the Laplacian of a graph.
- reorder.mean - compute the mean value of a vector.
- reorder.meancolumns - compute a column containing the means of a matrix's rows.
- reorder.meantranspose - compute the mean of a matrix column.
- reorder.poweriteration - compute the eigenvector with the largest eigenvalue from a symmetric definite positive matrix using a power iteration.
- [reorder.poweriteration_n](LinearAlgebra#poweriteration_n] - compute the n eigenvectors with the largest eivenvalues from a symmetric definite positive matrix using a power iteration.
- reorder.fix_distance_matrix - fix numerical precision issues with a computed distance matrix.
- reorder.check_distance_matrix - test if a matrix is symmetric definite positive.
- reorder.ca - compute the Correspondence Analysis (or decomposition) of a positive matrix.