def save_differential_expression_h5(f, clustering_key, de): group = f.create_group(f.root, analysis_constants.ANALYSIS_H5_DIFFERENTIAL_EXPRESSION_GROUP) analysis_io.save_h5(f, group, clustering_key, de) cr_clustering.create_legacy_kmeans_nodes(f, analysis_constants.ANALYSIS_H5_DIFFERENTIAL_EXPRESSION_GROUP, analysis_constants.ANALYSIS_H5_KMEANS_DIFFERENTIAL_EXPRESSION_GROUP, DIFFERENTIAL_EXPRESSION, clustering_key)
def save_kmeans_h5(f, n_clusters, kmeans): clustering_key = cr_clustering.format_clustering_key(cr_clustering.CLUSTER_TYPE_KMEANS, n_clusters) group = f.create_group(f.root, cr_constants.ANALYSIS_H5_CLUSTERING_GROUP) cr_io.save_h5(f, group, clustering_key, kmeans) cr_clustering.create_legacy_kmeans_nodes(f, cr_constants.ANALYSIS_H5_CLUSTERING_GROUP, cr_constants.ANALYSIS_H5_KMEANS_GROUP, cr_clustering.CLUSTERING, clustering_key)
def save_graphclust_h5(f, labels): clustering_key = cr_clustering.format_clustering_key( cr_clustering.CLUSTER_TYPE_GRAPHCLUST, 0) clustering = cr_clustering.create_clustering( clusters=labels, num_clusters=max(labels), cluster_score=0, clustering_type=cr_clustering.CLUSTER_TYPE_GRAPHCLUST, global_sort_key=float('-inf'), # always first description=cr_clustering.humanify_clustering_key(clustering_key)) group = f.create_group(f.root, cr_constants.ANALYSIS_H5_CLUSTERING_GROUP) cr_io.save_h5(f, group, clustering_key, clustering)
def save_pca_h5(pca_map, f): group = f.create_group(f.root, cr_constants.ANALYSIS_H5_PCA_GROUP) for n_components, pca in pca_map.iteritems(): cr_io.save_h5(f, group, str(n_components), pca)
def save_lsa_h5(lsa_map, f): group = f.create_group(f.root, analysis_constants.ANALYSIS_H5_LSA_GROUP) for n_components, lsa in lsa_map.iteritems(): analysis_io.save_h5(f, group, str(n_components), lsa)
def save_kmedoids_h5(f, n_clusters, kmedoids): clustering_key = cr_clustering.format_clustering_key(cr_clustering.CLUSTER_TYPE_KMEDOIDS, n_clusters) group = f.create_group(f.root, analysis_constants.ANALYSIS_H5_CLUSTERING_GROUP) analysis_io.save_h5(f, group, clustering_key, kmedoids)
def save_tsne_h5(tsne, f): """Save a TSNE object to HDF5""" group = f.create_group(f.root, analysis_constants.ANALYSIS_H5_TSNE_GROUP) analysis_io.save_h5(f, group, tsne.key, tsne)
def save_tsne_h5(tsne_map, f): group = f.create_group(f.root, cr_constants.ANALYSIS_H5_TSNE_GROUP) for n_tsne_components, tsne in tsne_map.iteritems(): cr_io.save_h5(f, group, str(n_tsne_components), tsne)