def analyze(input_data_path, output_image_path, tree_building_function):
logging.debug('read the matrix')
X = util.file_to_comma_separated_matrix(input_data_path, has_headers=True)
logging.debug('build the tree')
root = tree_building_function(X)
logging.debug('extract ordered indices from the tree')
ordered_indices = root.ordered_labels()
logging.debug('create the elementwise squared correlation matrix')
R = np.corrcoef(X)
logging.debug('permute the elementwise squared correlation matrix according to the ordering')
M = heatmap.get_permuted_rows_and_columns(R, ordered_indices)
logging.debug('create the heatmap')
f = gradient.correlation_to_rgb
heatmap.get_heatmap_with_dendrogram(M, root, f, output_image_path)
def main():
X = util.file_to_whitespace_separated_matrix("khatrisvd/fivetimes.txt")
n = len(X)
permutation = range(n)
random.shuffle(permutation)
X = heatmap.get_permuted_rows(X, permutation)
root = treebuilder.build_tree(X)
# show the unordered heatmap
filename = "unordered.png"
RoR = np.corrcoef(X) ** 2
heatmap.get_heatmap(RoR, filename)
# show the ordered heatmap
filename = "reordered.png"
ordered_indices = root.ordered_labels()
M = heatmap.get_permuted_rows_and_columns(RoR, ordered_indices)
heatmap.get_heatmap(M, filename)
