File size: 3,001 Bytes
e3814d7 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 | # This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
# --------------------------------------------------------
# References:
# HiCARN: https://github.com/OluwadareLab/HiCARN
# --------------------------------------------------------
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
def heatmap(ax, mat, title=None, x_label=None, y_label=None, show_bar=True, close_ticks=False):
cmap = "Reds"
vmin, vmax = 0, 0.5
im = ax.matshow(mat, interpolation='nearest', cmap=cmap, aspect='auto', vmin=vmin, vmax=vmax)
if show_bar:
cbar = plt.colorbar(im, ax=ax, aspect=9, shrink=0.3, ticks=[vmin, vmax])
cbar.ax.yaxis.set_ticks_position('none')
cbar.ax.set_yticklabels([])
cbar.ax.set_xlabel('Low', fontsize='large')
cbar.ax.set_title('High', fontsize='large')
cbar.ax.set_ylabel('reads', rotation=-90, va='bottom', fontsize='x-large')
if close_ticks:
ax.set_xticks([])
ax.set_yticks([])
if title is not None:
ax.set_title(title)
if x_label is not None:
ax.set_xlabel(x_label)
if y_label is not None:
ax.set_ylabel(y_label)
return im
def hic_heatmap(data, dediag=0, ncols=1, titles=None, x_labels=None, y_labels=None, file=None):
if isinstance(data, list):
axs = []
nrows = int(len(data) // ncols + 1)
figure = plt.figure(facecolor='w', figsize=(4.9 * ncols, 4 * nrows))
gs = gridspec.GridSpec(nrows, ncols)
for i, mat in enumerate(data):
row, col = i // ncols, i % ncols
axs.append(figure.add_subplot(gs[row, col]))
if dediag > 0 and mat.ndim == 2:
mat = np.triu(mat, dediag) + np.triu(mat.T, dediag).T
# only show details on the first row and the first column
title = titles[col] if titles is not None else None
y_label = y_labels[row] if col == 0 and y_labels is not None else None
x_label = x_labels[col] if row == 0 and x_labels is not None else None
heatmap(axs[-1], mat, title, x_label, y_label)
else:
figure = plt.figure(facecolor='w')
ax = figure.add_subplot(1, 1, 1)
if dediag > 0:
data = np.triu(data, dediag) + np.triu(data.T, dediag).T
heatmap(ax, data, title=titles, x_label=x_labels, y_label=y_labels)
figure.tight_layout()
if file is not None:
figure.savefig(file, format='svg')
def surf(data):
fig = plt.figure()
ax = fig.gca(projection='3d')
m, n = data.shape
x, y = np.meshgrid(range(m), range(n))
ax.plot_surface(x, y, data)
def _clear_max_min(x, y):
idx_x = np.where((x > x.min()) & (x < x.max()))[0]
idx_y = np.where((y > y.min()) & (y < y.max()))[0]
idx_setx, idx_sety = set(idx_x), set(idx_y)
inter_idx = np.array(list(idx_setx.intersection(idx_sety)))
return x[inter_idx], y[inter_idx]
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