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)