bplot = plt.boxplot([rdmavals, rdmbvals, corrvals],
showfliers=False,
positions=pos,
patch_artist=True,
widths=config['go_boxplot_width'],
medianprops=medianprops,
boxprops=boxprops,
whiskerprops=whiskerprops,
capprops=capprops,
flierprops=flierprops)
colors = [
config['rdm_a_boxplot_color'], config['rdm_b_boxplot_color'],
config['fc_path_boxplot_color']
]
utils.plot_significances_paths([rdmavals, rdmbvals, corrvals],
pos,
no_fliers=True)
for patch, color in zip(bplot['boxes'], colors):
patch.set_facecolor(color)
pos = pos + 3
if groups.shape[0] > 2:
plt.xticks(range(1, 3 * groups.shape[0] + 1),
create_labels(groups.group_label.tolist()))
else:
plt.xticks(range(1, 3 * groups.shape[0] + 1),
create_labels(groups.group_label.tolist()))
for lnx in np.arange(3.5, groups.shape[0] * 3, 3):
plt.axvline(lnx, linestyle=':', color='lightgray')
else:
plt.text(0, 0, 'No control group', fontsize=15, ha='center')
[asthma_pneumonia_disease, asthma_ipf_disease, asthma_copd_disease_4302],
showfliers=False,
positions=pos,
patch_artist=True,
widths=config['go_boxplot_width'],
medianprops=medianprops,
boxprops=boxprops,
whiskerprops=whiskerprops,
capprops=capprops,
flierprops=flierprops)
colors = [
config['pneumonia_boxplot_color'], config['ipf_boxplot_color'],
config['fc_path_boxplot_color']
]
utils.plot_significances_paths(
[asthma_pneumonia_disease, asthma_ipf_disease, asthma_copd_disease_4302],
pos,
no_fliers=True)
for patch, color in zip(bplot['boxes'], colors):
patch.set_facecolor(color)
plt.xticks(range(1, 4), labels)
plt.ylabel('Sequential coexpression', fontsize=12)
plt.title('SC in asthmatic patients (GSE4302)')
plt.tight_layout()
if not args.dry:
plt.savefig(out_file)
if not args.no_show:
plt.show()
capprops = {'linewidth': 1.}
medianprops = {'color': 'red', 'linewidth': 1.5, 'zorder': 6}
flierprops = {'marker': 'o', 'markeredgecolor': 'lightgray', 'zorder': 3}
bplot = plt.boxplot([typea_seqsims[i], typeb_seqsims[i], obs_seqsims[i]],
positions=pos,
showfliers=False,
patch_artist=True,
widths=0.3,
medianprops=medianprops,
boxprops=boxprops,
whiskerprops=whiskerprops,
capprops=capprops,
flierprops=flierprops)
utils.plot_significances_paths(
[typea_seqsims[i], typeb_seqsims[i], obs_seqsims[i]],
delta_ratio=30,
no_fliers=True)
colors = ['lightblue', 'lightblue', 'lightcoral']
for patch, color in zip(bplot['boxes'], colors):
patch.set_facecolor(color)
labels = ['Rdm\n(Type A)', 'Rdm\n(Type B)', 'FC paths']
plt.xticks(pos, labels, fontsize=10)
plt.gca().tick_params(axis='both', which='major', labelsize=5)
# plt.ylabel('Sequential GO similarity', fontsize=13);
# plt.ylim([None,9.3])
plt.title(ylbl_short[i], fontsize=7)
plt.suptitle('Sequential similarity of similar disease pairs',
fontsize=20,
y=1.02)
plt.tight_layout()
[copd_pneumonia_disease, copd_ipf_disease, asthma_copd_disease_57148],
showfliers=False,
positions=pos,
patch_artist=True,
widths=config['go_boxplot_width'],
medianprops=medianprops,
boxprops=boxprops,
whiskerprops=whiskerprops,
capprops=capprops,
flierprops=flierprops)
colors = [
config['pneumonia_boxplot_color'], config['ipf_boxplot_color'],
config['fc_path_boxplot_color']
]
utils.plot_significances_paths(
[copd_pneumonia_disease, copd_ipf_disease, asthma_copd_disease_57148],
pos,
no_fliers=True)
for patch, color in zip(bplot['boxes'], colors):
patch.set_facecolor(color)
plt.xticks(range(1, 4), labels)
plt.ylabel('Sequential coexpression', fontsize=12)
plt.title('SC in COPD patients (GSE57148)')
plt.tight_layout()
if not args.dry:
plt.savefig(out_file)
if not args.no_show:
plt.show()