def run(self):
"""
2008-09-10
in case chop the whole figure into blocks, swap col_block_index and row_block_index to make row first, column 2nd
"""
from SNP import read_data
from utils import figureOutDelimiter, PassingData
delimiter = figureOutDelimiter(self.input_fname)
print delimiter
header, row_label_ls1, row_label_ls2, data_matrix = read_data(
self.input_fname, matrix_data_type=float, delimiter="\t"
)
import numpy
data_matrix = numpy.array(data_matrix)
min_value = numpy.min(data_matrix)
if self.min_value_non_negative and min_value < 0:
min_value = 0
max_value = numpy.max(data_matrix)
font = get_font(self.font_path, font_size=self.font_size)
Value2Color.special_value2color[-2] = self.super_value_color
value2color_func = lambda x: Value2Color.value2HSLcolor(x, min_value, max_value)
im_legend = drawContinousLegend(min_value, max_value, self.no_of_ticks, value2color_func, font)
fig_fname_prefix = os.path.splitext(self.fig_fname)[0]
if self.split_legend_and_matrix:
im_legend.save("%s_legend.png" % fig_fname_prefix)
no_of_rows, no_of_cols = data_matrix.shape
passParam = PassingData(
value2color_func=value2color_func,
im_legend=im_legend,
font=font,
split_legend_and_matrix=self.split_legend_and_matrix,
no_grid=self.no_grid,
)
if no_of_cols <= self.col_step_size:
self._drawMatrix(data_matrix, row_label_ls1, header[2:], self.fig_fname, passParam)
else: # split into blocks
no_of_col_blocks = no_of_cols / self.col_step_size + 1
no_of_row_blocks = no_of_rows / self.row_step_size + 1
for i in range(no_of_col_blocks):
col_start_index = i * self.col_step_size
col_end_index = (i + 1) * self.col_step_size
if col_start_index < no_of_cols:
for j in range(no_of_row_blocks):
row_start_index = j * self.row_step_size
row_end_index = (j + 1) * self.row_step_size
if row_start_index < no_of_rows:
fig_fname = "%s_%s_%s.png" % (fig_fname_prefix, j, i) # row first, column 2nd
self._drawMatrix(
data_matrix[row_start_index:row_end_index, col_start_index:col_end_index],
row_label_ls1[row_start_index:row_end_index],
header[2 + col_start_index : 2 + col_end_index],
fig_fname,
passParam,
)
def readInRawMatrixData(self, input_fname): """ 2009-3-13 """ delimiter = figureOutDelimiter(input_fname) self.header, self.strain_acc_list, self.category_list, self.data_matrix = read_data(input_fname, delimiter=delimiter)
