Python get_nonphylogenetic_metric Examples

Example #1

File: make_otu_heatmap.py Project: jrherr/qiime

def get_clusters(x_original, axis=['row', 'column'][0]):
    """Performs UPGMA clustering using euclidean distances"""
    x = x_original.copy()
    if axis == 'column':
        x = x.T
    nr = x.shape[0]
    metric_f = get_nonphylogenetic_metric('euclidean')
    row_dissims = DistanceMatrix(metric_f(x), map(str, range(nr)))
    # do upgma - rows
    # Average in SciPy's cluster.heirarchy.linkage is UPGMA
    linkage_matrix = linkage(row_dissims.condensed_form(), method='average')
    tree = TreeNode.from_linkage_matrix(linkage_matrix, row_dissims.ids)
    row_order = [int(tip.name) for tip in tree.tips()]
    return row_order

Example #2

def get_clusters(x_original, axis=['row', 'column'][0]):
    """Performs UPGMA clustering using euclidean distances"""
    x = x_original.copy()
    if axis == 'column':
        x = x.T
    nr = x.shape[0]
    metric_f = get_nonphylogenetic_metric('euclidean')
    row_dissims = DistanceMatrix(metric_f(x), map(str, range(nr)))
    # do upgma - rows
    # Average in SciPy's cluster.heirarchy.linkage is UPGMA
    linkage_matrix = linkage(row_dissims.condensed_form(), method='average')
    tree = TreeNode.from_linkage_matrix(linkage_matrix, row_dissims.ids)
    row_order = [int(tip.name) for tip in tree.tips()]
    return row_order

Example #3

File: make_otu_heatmap.py Project: Ecogenomics/FrankenQIIME

def get_clusters(x_original, axis=['row','column'][0]):
    """Performs UPGMA clustering using euclidean distances"""
    x = x_original.copy()
    if axis=='column':
        x = x.T
    nr = x.shape[0]
    metric_f = get_nonphylogenetic_metric('euclidean')
    row_dissims = metric_f(x)
    # do upgma - rows
    BIG = 1e305
    row_nodes = map(PhyloNode, map(str,range(nr)))
    for i in range(len(row_dissims)):
        row_dissims[i,i] = BIG
    row_tree = UPGMA_cluster(row_dissims, row_nodes, BIG)
    row_order = [int(tip.Name) for tip in row_tree.iterTips()]
    return row_order

Example #4

File: make_otu_heatmap.py Project: franny911/qiime

def get_clusters(x_original, axis=['row', 'column'][0]):
    """Performs UPGMA clustering using euclidean distances"""
    x = x_original.copy()
    if axis == 'column':
        x = x.T
    nr = x.shape[0]
    metric_f = get_nonphylogenetic_metric('euclidean')
    row_dissims = metric_f(x)
    # do upgma - rows
    BIG = 1e305
    row_nodes = map(PhyloNode, map(str, range(nr)))
    for i in range(len(row_dissims)):
        row_dissims[i, i] = BIG
    row_tree = UPGMA_cluster(row_dissims, row_nodes, BIG)
    row_order = [int(tip.Name) for tip in row_tree.iterTips()]
    return row_order