def draw_read_pos_stats(stats, plot_fhand):
n_read_groups = len(stats['5_read_pos_counts'])
figure, canvas = get_fig_and_canvas(n_read_groups, 2)
n_plot = 0
for read_group in stats['5_read_pos_counts'].keys():
rg_stat = {
'5_read_pos_counts': stats['5_read_pos_counts'][read_group],
'3_read_pos_counts': stats['3_read_pos_counts'][read_group],
'5_read_pos_boxplot': stats['5_read_pos_boxplot'][read_group],
'3_read_pos_boxplot': stats['3_read_pos_boxplot'][read_group]
}
n_plot += 1
axes1 = figure.add_subplot(n_read_groups, 2, n_plot)
if read_group is None:
title = "Pos. counted from 5'"
else:
title = "Pos. counted from 5' (rg: {})".format(read_group)
_draw_one_read_pos_stats(rg_stat, axes1, '5_read_pos_boxplot',
'5_read_pos_counts', title)
if read_group is None:
title = "Pos. counted from 3'"
else:
title = "Pos. counted from 3' (rg: {})".format(read_group)
n_plot += 1
axes2 = figure.add_subplot(n_read_groups, 2, n_plot)
_draw_one_read_pos_stats(rg_stat, axes2, '3_read_pos_boxplot',
'3_read_pos_counts', title)
canvas.print_figure(plot_fhand)
plot_fhand.flush()
def draw_read_pos_stats(stats, plot_fhand):
n_read_groups = len(stats['5_read_pos_counts'])
figure, canvas = get_fig_and_canvas(n_read_groups, 2)
n_plot = 0
for read_group in stats['5_read_pos_counts'].keys():
rg_stat = {'5_read_pos_counts': stats['5_read_pos_counts'][read_group],
'3_read_pos_counts': stats['3_read_pos_counts'][read_group],
'5_read_pos_boxplot': stats['5_read_pos_boxplot'][read_group],
'3_read_pos_boxplot': stats['3_read_pos_boxplot'][read_group]}
n_plot += 1
axes1 = figure.add_subplot(n_read_groups, 2, n_plot)
if read_group is None:
title = "Pos. counted from 5'"
else:
title = "Pos. counted from 5' (rg: {})".format(read_group)
_draw_one_read_pos_stats(rg_stat, axes1, '5_read_pos_boxplot',
'5_read_pos_counts', title)
if read_group is None:
title = "Pos. counted from 3'"
else:
title = "Pos. counted from 3' (rg: {})".format(read_group)
n_plot += 1
axes2 = figure.add_subplot(n_read_groups, 2, n_plot)
_draw_one_read_pos_stats(rg_stat, axes2, '3_read_pos_boxplot',
'3_read_pos_counts', title)
canvas.print_figure(plot_fhand)
plot_fhand.flush()
def plot_in_genome(iterator, out_base, labels):
xsize = 100
ysize = 10
for chrom, x_vals, y_vals in window_data_by_chrom(iterator):
fig, canvas = get_fig_and_canvas(figsize=(xsize, ysize))
num_axes = len(y_vals)
for index, plotname in enumerate(labels.keys()):
plot_label = labels[plotname]
axes = fig.add_subplot(num_axes, 1, index + 1)
axes.plot(x_vals, y_vals[plotname])
title = plot_label['title'] + ' for chromosome {}'.format(chrom)
axes.set_title(title)
axes.set_ylabel(plot_label['ylabel'])
axes.set_xlabel('Position in chromosome')
fhand = open(out_base + '.' + str(chrom) + '.png', 'w')
canvas.print_figure(fhand, dpi=300)
fhand.flush()
def plot_in_genome(iterator, out_base, labels):
xsize = 100
ysize = 10
for chrom, x_vals, y_vals in window_data_by_chrom(iterator):
fig, canvas = get_fig_and_canvas(figsize=(xsize, ysize))
num_axes = len(y_vals)
for index, plotname in enumerate(labels.keys()):
plot_label = labels[plotname]
axes = fig.add_subplot(num_axes, 1, index + 1)
axes.plot(x_vals, y_vals[plotname])
title = plot_label['title'] + ' for chromosome {}'.format(chrom)
axes.set_title(title)
axes.set_ylabel(plot_label['ylabel'])
axes.set_xlabel('Position in chromosome')
fhand = open(out_base + '.' + str(chrom) + '.png', 'w')
canvas.print_figure(fhand, dpi=300)
fhand.flush()
