def main(args):
numerator_seq_files_data, denominator_seq_files_data, matrix_params, heatmap_params, filenames, max_threads = get_args(
args)
# Get the fold change matrix
fold_change_matrix = get_fold_change_matrix(numerator_seq_files_data,
denominator_seq_files_data,
matrix_params, filenames,
max_threads)
# Now plot!
bp_width, width, height, max_log2_fc, interval_size, minor_ticks, major_ticks = heatmap_params
output_prefix = filenames[-1]
output_filename = output_prefix + "_max_" + str(max_log2_fc) + "_width_" + str(bp_width) + \
"bp_fold_change_TES_heatmap"
only_heatmap_filename = generate_random_filename(".tiff")
negative_log2_value = -1 * max_log2_fc if max_log2_fc else None
generate_heatmap(fold_change_matrix, 'red/blue', only_heatmap_filename,
2.2, negative_log2_value, max_log2_fc)
tick_params = (minor_ticks, major_ticks)
ticks_image_filename = make_ticks_image(width, interval_size, tick_params)
combine_images(ticks_image_filename, only_heatmap_filename,
output_filename)
remove_files(fold_change_matrix, ticks_image_filename,
only_heatmap_filename)
def make_rgb_heatmap(fold_change_matrix_filename, heatmap_params,
output_filename_prefix):
bp_width, width, height, gamma, max_fold_change, interval_size, minor_ticks_bp, major_ticks_bp = heatmap_params
tick_params = minor_ticks_bp, major_ticks_bp
only_heatmap_filename = generate_random_filename(extension=".tiff")
if max_fold_change != None:
negative_max_fold_change = -1 * max_fold_change
else:
negative_max_fold_change = None
generate_heatmap(fold_change_matrix_filename,
'red/blue',
only_heatmap_filename,
gamma,
negative_max_fold_change,
max_fold_change,
ticks=None)
ticks_image_filename = make_ticks_image(width, interval_size, tick_params)
# Combine the two images together
output_filename = output_filename_prefix + "_max_" + str(
max_fold_change) + "_width_" + str(
bp_width) + "bp_gene_body_fold_change_heatmap"
combine_images(ticks_image_filename, only_heatmap_filename,
output_filename)
remove_files(fold_change_matrix_filename, ticks_image_filename,
only_heatmap_filename)
def make_heatmap(matrix, heatmap_params, output_filename_prefix):
bp_width, width, height, gamma, max_black_value, interval_size, minor_ticks_bp, major_ticks_bp = heatmap_params
# Minor tick marks every 10 kb and major tick marks every 50 kb
t = Ticks(minor_tick_mark_interval_size=(minor_ticks_bp / interval_size),
major_tick_mark_interval_size=(major_ticks_bp / interval_size))
output_filename = output_filename_prefix + "_max_" + str(
max_black_value) + "_gamma_" + str(gamma) + "_width_" + str(
bp_width) + "bp_TES_heatmap.tiff"
generate_heatmap(matrix,
'gray',
output_filename,
gamma,
0,
max_black_value,
ticks=t)
def make_heatmap(log2_matrix, max_log2_fold_change, tick_parameters, output_filename, px_per_bp):
# Define gamma as 2.2 even though it won't be used
gamma = 2.2
min_value = -1 * max_log2_fold_change if max_log2_fold_change else None
max_value = max_log2_fold_change
red_blue_image = generate_random_filename('.tiff')
if tick_parameters != (None, None):
# Get the width of the matrix so we can make the ticks
with open(log2_matrix) as file:
width = len(file.readline().split())
ticks_image = make_ticks_image(width, tick_parameters, px_per_bp)
generate_heatmap(log2_matrix, 'red/blue', red_blue_image, gamma, min_value, max_value)
combine_images(ticks_image, red_blue_image, output_filename)
else:
generate_heatmap(log2_matrix, 'red/blue', output_filename, gamma, min_value, max_value)
def make_heatmap(matrix_filename, output_prefix, heatmap_parameters,
tick_parameters):
max_value, gamma = heatmap_parameters
# Now make the heatmap
min_value = None
output_filename = output_prefix + "_max_" + str(
max_value) + "_gamma_" + str(gamma) + "_region_heatmap.tiff"
if tick_parameters != (None, None):
ticks = Ticks(*tick_parameters, offset=1)
else:
ticks = None
generate_heatmap(matrix_filename,
'gray',
output_filename,
gamma,
min_value,
max_value,
ticks=ticks)