def _load_dimensionality_reduced_matrix_h5(self, group):
if self.method == 'pca':
for n_components, pca in analysis_io.load_h5_iter(group, PCA):
self.dimensionality_reducted_matrix[int(n_components)] = pca
return
elif self.method == 'lsa':
for n_components, lsa in analysis_io.load_h5_iter(group, LSA):
self.dimensionality_reducted_matrix[int(n_components)] = lsa
return
elif self.method == 'plsa':
for n_components, plsa in analysis_io.load_h5_iter(group, PLSA):
self.dimensionality_reducted_matrix[int(n_components)] = plsa
return
raise ValueError('method {} not allowed'.format(self.method))
def load_pca_from_h5(filename):
""" Load just the PCA info from an analysis h5 """
with tables.open_file(filename, 'r') as f:
group = f.root._v_groups[cr_constants.ANALYSIS_H5_PCA_GROUP]
# Just take the first PCA object, assuming we never have multiple
for _, pca in cr_io.load_h5_iter(group, PCA):
return pca
def load_lsa_from_h5(filename):
""" Load just the LSA info from an analysis h5 """
with tables.open_file(filename, 'r') as f:
group = f.root._v_groups[analysis_constants.ANALYSIS_H5_LSA_GROUP]
# Just take the first LSA object, assuming we never have multiple
for _, lsa in analysis_io.load_h5_iter(group, LSA):
return lsa
def load_graphclust_from_h5(filename):
with tables.open_file(filename, 'r') as f:
group = f.root._v_groups[cr_constants.ANALYSIS_H5_CLUSTERING_GROUP]
# Take the first entry
for key, clustering in cr_io.load_h5_iter(group,
cr_clustering.CLUSTERING):
clustering_type, _ = cr_clustering.parse_clustering_key(key)
if clustering_type == cr_clustering.CLUSTER_TYPE_GRAPHCLUST:
return clustering
def _load_tsne_h5(self, group):
for _, tsne in analysis_io.load_h5_iter(group, TSNE):
self.tsne[tsne.key] = tsne
def _load_differential_expression_h5(self, group):
for clustering_key, de in analysis_io.load_h5_iter(
group, DIFFERENTIAL_EXPRESSION):
self.differential_expression[clustering_key] = de
def _load_clustering_h5(self, group):
for clustering_key, clustering in analysis_io.load_h5_iter(
group, cr_clustering.CLUSTERING):
self.clusterings[clustering_key] = clustering