def main():
# read the data matrix from stdin
logging.debug('reading input lines')
lines = sys.stdin.readlines()
logging.debug('converting input lines to data matrix')
X = util.lines_to_comma_separated_matrix(lines, has_headers=True)
logging.debug('creating the tree')
root = treebuilder.build_tree(X)
logging.debug('creating the newick string')
print root.get_newick_string()
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)
def main():
pathname_in = 'mmc-data-files/Starvation_Residual.TXT'
X = util.file_to_comma_separated_matrix(pathname_in, has_headers=True)
print X.shape
# create the tree from the data
root = treebuilder.build_tree(X)
ordered_indices = root.ordered_labels()
X = heatmap.get_permuted_rows(X, ordered_indices)
# create the standardized data for drawing the small heatmap
Z = khorr.get_standardized_matrix(X)
# show the big heatmap
pathname_out = 'big.png'
color_function = gradient.correlation_to_rgb
im = heatmap.get_heatmap_image(np.dot(Z, Z.T), color_function)
fout = open(pathname_out, 'wb')
im.save(fout)
fout.close()
# show the small heatmap
pathname_out = 'small.png'
im = heatmap.get_reduced_heatmap_image(Z, reduction=5)
fout = open(pathname_out, 'wb')
im.save(fout)
fout.close()