code stringlengths 3 6.57k |
|---|
_dfs(clade_b) |
_dfs(root) |
getTreeFromLinkage(names, linkage) |
isinstance(linkage, np.ndarray) |
TypeError('linkage must be a numpy.ndarray instance') |
LinkageError('linkage must be a 2-dimensional matrix') |
LinkageError('linkage must have exactly 4 columns') |
len(names) |
LinkageError('linkage must have exactly len(names) |
Clade(None, name) |
clades.append(clade) |
heights.append(0.) |
int(link[0]) |
int(link[1]) |
Clade(None, None) |
clade.clades.append(left) |
clade.clades.append(right) |
clades.append(clade) |
heights.append(height) |
Tree(clade) |
calcTree(names, distance_matrix, method='upgma', linkage=False) |
len(names) |
len(names) |
ValueError("Mismatch between the sizes of matrix and names.") |
method.lower() |
strip() |
hlinkage(squareform(distance_matrix) |
getTreeFromLinkage(names, Z) |
matrix.append(list(row[:k]) |
isinstance(names, np.ndarray) |
names.tolist() |
DistanceMatrix(names, matrix) |
DistanceTreeConstructor() |
method.strip() |
lower() |
constructor.nj(dm) |
constructor.upgma(dm) |
getLinkage(names, tree) |
tree.get_nonterminals() |
writeTree(filename, tree, format_str='newick') |
isinstance(filename, str) |
TypeError('filename should be a string') |
isinstance(tree, Phylo.BaseTree.Tree) |
TypeError('tree should be a Biopython.Phylo Tree object') |
isinstance(format_str, str) |
TypeError('format_str should be a string') |
Phylo.write(tree, filename, format_str) |
clusterMatrix(distance_matrix=None, similarity_matrix=None, labels=None, return_linkage=None, **kwargs) |
labels (if **labels** are passed) |
matrix (if **return_linkage** is **True**) |
ValueError('Please provide a distance matrix or a similarity matrix') |
kwargs.pop('orientiation', 'right') |
kwargs.pop('reversed', False) |
kwargs.pop('no_plot', True) |
spatial.distance.squareform(distance_matrix) |
sch.linkage(formatted_distance_matrix, **kwargs) |
sch.dendrogram(linkage_matrix, orientation=orientation, labels=labels, no_plot=no_plot) |
return_vals.append(sorted_labels) |
return_vals.append(linkage_matrix) |
tuple(return_vals) |
showLines(*args, **kwargs) |
band(s) |
band(s) |
kwargs.pop('ticklabels', None) |
kwargs.pop('dy', None) |
kwargs.pop('lower', None) |
kwargs.pop('upper', None) |
kwargs.pop('alpha', 0.5) |
kwargs.pop('beta', 0.25) |
kwargs.pop('gap', False) |
kwargs.pop('label', None) |
gca() |
ax.plot(*args, **kwargs) |
enumerate(lines) |
line.get_color() |
line.get_data() |
addEnds(x, y) |
line.set_data(x_new, y_new) |
np.isscalar(labels) |
line.set_label(labels) |
line.set_label(labels[i]) |
ValueError('The number of labels ({0}) |
y ({1}) |
format(len(labels) |
len(line) |
sub_array(a, i, tag='a') |
np.isscalar(a[0]) |
list (array) |
list (array) |
ValueError('The number of {2} ({0}) |
y ({1}) |
format(len(miny) |
len(line) |
len(_a) |
len(y) |
ValueError('The shapes of {2} ({0}) |
y ({1}) |
format(len(_miny) |
len(y) |
sub_array(miny, i) |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.