def save_coord(results_dirpath, coord_x, coord_y, name_coord,
contigs_fpaths): # coordinates for Nx, NAx, NGx, NGAX
json_fpath = json_saver.save_coord(results_dirpath, coord_x, coord_y,
name_coord, contigs_fpaths)
if json_fpath:
append(results_dirpath, json_fpath, name_coord)
def Nx_plot(results_dir, reduce_points, contigs_fpaths, lists_of_lengths, plot_fpath, title='Nx', reference_lengths=None, json_output_dir=None):
if can_draw_plots:
logger.info(' Drawing ' + title + ' plot...')
import matplotlib.pyplot
import matplotlib.ticker
figure = matplotlib.pyplot.figure()
matplotlib.pyplot.rc('font', **font)
max_y = 0
color_id = 0
json_vals_x = [] # coordinates for Nx-like plots in HTML-report
json_vals_y = []
for id, (contigs_fpath, lengths) in enumerate(itertools.izip(contigs_fpaths, lists_of_lengths)):
if not lengths:
json_vals_x.append([])
json_vals_y.append([])
continue
vals_x = [0.0]
vals_y = [lengths[0]]
lengths.sort(reverse=True)
# calculate values for the plot
vals_Nx = [0.0]
vals_l = [lengths[0]]
lcur = 0
# if Nx-plot then we just use sum of contigs lengths, else use reference_length
lsum = sum(lengths)
if reference_lengths:
lsum = reference_lengths[id]
min_difference = 0
if reduce_points:
min_difference = qconfig.min_difference
for l in lengths:
lcur += l
x = lcur * 100.0 / lsum
if can_draw_plots:
vals_Nx.append(vals_Nx[-1] + 1e-10) # eps
vals_l.append(l)
vals_Nx.append(x)
vals_l.append(l)
if vals_y[-1] - l > min_difference or len(vals_x) == 1:
vals_x.append(vals_x[-1] + 1e-10) # eps
vals_y.append(l)
vals_x.append(x)
vals_y.append(l)
# add to plot
json_vals_x.append(vals_x)
json_vals_y.append(vals_y)
if can_draw_plots:
vals_Nx.append(vals_Nx[-1] + 1e-10) # eps
vals_l.append(0.0)
vals_x.append(vals_x[-1] + 1e-10) # eps
vals_y.append(0.0)
max_y = max(max_y, max(vals_l))
color, ls = get_color_and_ls(contigs_fpath)
matplotlib.pyplot.plot(vals_Nx, vals_l, color=color, lw=line_width, ls=ls)
if qconfig.html_report:
from quast_libs.html_saver import html_saver
html_saver.save_coord(results_dir, json_vals_x, json_vals_y, 'coord' + title, contigs_fpaths)
if json_output_dir:
from quast_libs.html_saver import json_saver
json_saver.save_coord(json_output_dir, json_vals_x, json_vals_y, title, contigs_fpaths)
if not can_draw_plots:
return
if with_title:
matplotlib.pyplot.title(title)
matplotlib.pyplot.grid(with_grid)
ax = matplotlib.pyplot.gca()
# Shink current axis's height by 20% on the bottom
box = ax.get_position()
ax.set_position([box.x0, box.y0 + box.height * 0.2, box.width, box.height * 0.8])
legend_list = map(qutils.label_from_fpath, contigs_fpaths)
# Put a legend below current axis
try: # for matplotlib <= 2009-12-09
ax.legend(legend_list, loc='upper center', bbox_to_anchor=(0.5, -0.1), fancybox=True,
shadow=True, ncol=n_columns if n_columns<3 else 3)
except Exception:
pass
ylabel = 'Contig length '
ylabel, mkfunc = y_formatter(ylabel, max_y)
matplotlib.pyplot.xlabel('x', fontsize=axes_fontsize)
matplotlib.pyplot.ylabel(ylabel, fontsize=axes_fontsize)
mkformatter = matplotlib.ticker.FuncFormatter(mkfunc)
ax.yaxis.set_major_formatter(mkformatter)
matplotlib.pyplot.xlim([0, 100])
#ax.invert_xaxis()
#matplotlib.pyplot.ylim(matplotlib.pyplot.ylim()[::-1])
xLocator, yLocator = get_locators()
ax.yaxis.set_major_locator(yLocator)
ax.xaxis.set_major_locator(xLocator)
plot_fpath += '.' + qconfig.plot_extension
matplotlib.pyplot.savefig(plot_fpath, bbox_inches='tight')
logger.info(' saved to ' + plot_fpath)
pdf_plots_figures.append(figure)
matplotlib.pyplot.close()
def save_coord(results_dirpath, coord_x, coord_y, name_coord, contigs_fpaths): # coordinates for Nx, NAx, NGx, NGAX
json_fpath = json_saver.save_coord(results_dirpath, coord_x, coord_y, name_coord, contigs_fpaths)
if json_fpath:
append(results_dirpath, json_fpath, name_coord)
def Nx_plot(results_dir, reduce_points, contigs_fpaths, lists_of_lengths, plot_fpath, title='Nx', reference_lengths=None, json_output_dir=None):
if can_draw_plots:
logger.info(' Drawing ' + title + ' plot...')
import matplotlib.pyplot
import matplotlib.ticker
figure = matplotlib.pyplot.figure()
matplotlib.pyplot.rc('font', **font)
max_y = 0
color_id = 0
json_vals_x = [] # coordinates for Nx-like plots in HTML-report
json_vals_y = []
for id, (contigs_fpath, lengths) in enumerate(zip(contigs_fpaths, lists_of_lengths)):
if not lengths:
json_vals_x.append([])
json_vals_y.append([])
continue
vals_x = [0.0]
vals_y = [lengths[0]]
lengths.sort(reverse=True)
# calculate values for the plot
vals_Nx = [0.0]
vals_l = [lengths[0]]
lcur = 0
# if Nx-plot then we just use sum of contigs lengths, else use reference_length
lsum = sum(lengths)
if reference_lengths:
lsum = reference_lengths[id]
min_difference = 0
if reduce_points:
min_difference = qconfig.min_difference
for l in lengths:
lcur += l
x = lcur * 100.0 / lsum
if can_draw_plots:
vals_Nx.append(vals_Nx[-1] + 1e-10) # eps
vals_l.append(l)
vals_Nx.append(x)
vals_l.append(l)
if vals_y[-1] - l > min_difference or len(vals_x) == 1:
vals_x.append(vals_x[-1] + 1e-10) # eps
vals_y.append(l)
vals_x.append(x)
vals_y.append(l)
# add to plot
json_vals_x.append(vals_x)
json_vals_y.append(vals_y)
if can_draw_plots:
vals_Nx.append(vals_Nx[-1] + 1e-10) # eps
vals_l.append(0.0)
vals_x.append(vals_x[-1] + 1e-10) # eps
vals_y.append(0.0)
max_y = max(max_y, max(vals_l))
color, ls = get_color_and_ls(contigs_fpath)
matplotlib.pyplot.plot(vals_Nx, vals_l, color=color, lw=line_width, ls=ls)
if qconfig.html_report:
from quast_libs.html_saver import html_saver
html_saver.save_coord(results_dir, json_vals_x, json_vals_y, 'coord' + title, contigs_fpaths)
if json_output_dir:
from quast_libs.html_saver import json_saver
json_saver.save_coord(json_output_dir, json_vals_x, json_vals_y, title, contigs_fpaths)
if not can_draw_plots:
return
if with_title:
matplotlib.pyplot.title(title)
matplotlib.pyplot.grid(with_grid)
ax = matplotlib.pyplot.gca()
# Shink current axis's height by 20% on the bottom
box = ax.get_position()
ax.set_position([box.x0, box.y0 + box.height * 0.2, box.width, box.height * 0.8])
legend_list = [qutils.label_from_fpath(fpath) for fpath in contigs_fpaths]
# Put a legend below current axis
try: # for matplotlib <= 2009-12-09
ax.legend(legend_list, loc='upper center', bbox_to_anchor=(0.5, -0.1), fancybox=True,
shadow=True, ncol=n_columns if n_columns<3 else 3)
except Exception:
pass
ylabel = 'Contig length '
ylabel, mkfunc = y_formatter(ylabel, max_y)
matplotlib.pyplot.xlabel('x', fontsize=axes_fontsize)
matplotlib.pyplot.ylabel(ylabel, fontsize=axes_fontsize)
mkformatter = matplotlib.ticker.FuncFormatter(mkfunc)
ax.yaxis.set_major_formatter(mkformatter)
matplotlib.pyplot.xlim([0, 100])
#ax.invert_xaxis()
#matplotlib.pyplot.ylim(matplotlib.pyplot.ylim()[::-1])
xLocator, yLocator = get_locators()
ax.yaxis.set_major_locator(yLocator)
ax.xaxis.set_major_locator(xLocator)
plot_fpath += '.' + qconfig.plot_extension
matplotlib.pyplot.savefig(plot_fpath, bbox_inches='tight')
logger.info(' saved to ' + plot_fpath)
pdf_plots_figures.append(figure)
matplotlib.pyplot.close()