From 0c1a3aafb036930b3558d8465066fc3dee8a6165 Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@cam.ac.uk>
Date: Tue, 1 Aug 2017 10:55:12 +0100
Subject: [PATCH] update names and docstrings to match what is actually read.
---
.../clusteringanalysis/dendrogramplotting.py | 6 ++++++
solventmapcreator/clusteringanalysis/matrixinput.py | 9 +++++----
.../test/clusteringanalysistest/matrixinputtest.py | 8 ++++----
3 files changed, 15 insertions(+), 8 deletions(-)
diff --git a/solventmapcreator/clusteringanalysis/dendrogramplotting.py b/solventmapcreator/clusteringanalysis/dendrogramplotting.py
index bbe2709..46aee67 100644
--- a/solventmapcreator/clusteringanalysis/dendrogramplotting.py
+++ b/solventmapcreator/clusteringanalysis/dendrogramplotting.py
@@ -16,6 +16,12 @@ logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
+def create_dendogram(linkage_matrix, labels, figsize):
+ """Creates a
+ """
+ dendrogram_plot, dendrogram_plot_axis = create_plot_with_axis(figsize)
+ cluster.dendrogram(linkage_matrix, labels=labels, ax=dendrogram_plot_axis)
+
def create_plot_with_axis(figsize):
"""Function creates plot and plot axis.
"""
diff --git a/solventmapcreator/clusteringanalysis/matrixinput.py b/solventmapcreator/clusteringanalysis/matrixinput.py
index 5e5185d..a29b4f1 100644
--- a/solventmapcreator/clusteringanalysis/matrixinput.py
+++ b/solventmapcreator/clusteringanalysis/matrixinput.py
@@ -16,20 +16,21 @@ logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
-def parse_similarity_matrix_file_trig_matrix(filename):
- """This reads a file into a dictionary, then appends the trigonal dictionary.
+def parse_similarity_matrix_file_condensed_matrix(filename):
+ """This reads a file into a dictionary, then appends the condensed matrix
+ to the dictionary.
"""
similarity_matrix_info = parse_similarity_matrix_file(filename)
append_condensed_matrix(similarity_matrix_info)
return similarity_matrix_info
def append_condensed_matrix(similarity_matrix_info):
- """This appends a triagonal matrix to the input dict.
+ """This appends a condensed matrix to the input dict.
"""
similarity_matrix_info["condensed_matrix"] = convert_to_condensed_matrix(similarity_matrix_info["value_matrix"])
def convert_to_condensed_matrix(similarity_matrix):
- """This converts the matrix to a triangular matrix.
+ """This converts the matrix to a condensed matrix.
"""
return scidist.squareform(similarity_matrix)
diff --git a/solventmapcreator/test/clusteringanalysistest/matrixinputtest.py b/solventmapcreator/test/clusteringanalysistest/matrixinputtest.py
index a364bc9..73c57a1 100644
--- a/solventmapcreator/test/clusteringanalysistest/matrixinputtest.py
+++ b/solventmapcreator/test/clusteringanalysistest/matrixinputtest.py
@@ -31,7 +31,7 @@ class MatrixInputTestCase(unittest.TestCase):
"""
del self.input_filename
del self.expected_dict
- def test_parse_similarity_matrix_file_trig_matrix(self):
+ def test_parse_similarity_matrix_file_condensed_matrix(self):
"""Test to see if expected dictionary is produced.
"""
expected_dict = {"labels":["poly_fit", "poly_fit2", "poly_fit3"],
@@ -39,14 +39,14 @@ class MatrixInputTestCase(unittest.TestCase):
[1.0, 0.0, 3.0],
[4.0, 3.0, 0.0]]),
"condensed_matrix":np.array([1.0, 4.0, 3.0])}
- actual_dict = matrixinput.parse_similarity_matrix_file_trig_matrix(self.input_filename)
+ actual_dict = matrixinput.parse_similarity_matrix_file_condensed_matrix(self.input_filename)
self.assertListEqual(sorted(expected_dict.keys()), sorted(actual_dict.keys()))
self.assertListEqual(expected_dict["labels"], actual_dict["labels"])
np.testing.assert_array_almost_equal(expected_dict["value_matrix"],
actual_dict["value_matrix"])
np.testing.assert_array_almost_equal(expected_dict["condensed_matrix"],
actual_dict["condensed_matrix"])
- def test_append_trigonal_matrix(self):
+ def test_append_condensed_matrix(self):
"""Test to see if matrix is appended as expected.
"""
expected_dict = {"labels":["poly_fit", "poly_fit2", "poly_fit3"],
@@ -61,7 +61,7 @@ class MatrixInputTestCase(unittest.TestCase):
expected_dict["value_matrix"])
np.testing.assert_array_almost_equal(self.expected_dict["condensed_matrix"],
expected_dict["condensed_matrix"])
- def test_convert_to_triangular_matrix(self):
+ def test_convert_to_condensed_matrix(self):
"""Test to see if expected matrix is returned.
"""
expected_matrix = np.array([1.0, 4.0, 3.0])
--
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