Moved plot functions into own script and began 1st results figure.

python/plot_functions.py

@@ -0,0 +1,128 @@
+import string
+import numpy as np
+import matplotlib.pyplot as plt
+from itertools import product
+
+def prepare_fig(nrows, ncols, width=8, height=None, rheight=2, unit=1/2.54,
+                left=0.01, right=0.95, bottom=0.01, top=0.95,
+                wspace=0.4, hspace=0.4):
+    if height is None:
+        height = rheight * nrows
+    fig = plt.figure(figsize=(width * unit, height * unit))
+    grid = fig.add_gridspec(nrows=nrows, ncols=ncols, wspace=wspace, hspace=hspace,
+                            left=left, right=right, top=top, bottom=bottom)
+    axes = np.zeros((nrows, ncols), dtype=object)
+    for i, j in product(range(nrows), range(ncols)):
+        axes[i, j] = fig.add_subplot(grid[i, j])
+        axes[i, j].set_facecolor('none')
+    return fig, axes
+
+def hide_axis(ax, side='bottom'):
+    ax.spines[side].set_visible(False)
+    params = {side: False, 'label' + side: False}
+    ax.tick_params(axis='x' if side in ['top', 'bottom'] else 'y',
+                   which='both', **params)
+    return None
+
+def letter_subplots(axes, labels=None, x=0.02, y=1, ha='left', va='bottom',
+                    fontsize=16, fontweight='bold', **kwargs):
+    if labels is None:
+        labels = string.ascii_lowercase
+    for ax, label in zip(axes, labels):
+        ax.text(x, y, label, transform=ax.transAxes, ha=ha, va=va,
+                fontsize=fontsize, fontweight=fontweight, **kwargs)
+    return None
+
+def xlimits(ax, time, minval=None, maxval=None, pad=0.05):
+    limits = [minval, maxval]
+    if minval is None:
+        limits[0] = time[0]
+    if maxval is None:
+        limits[1] = time[-1]
+    span = limits[1] - limits[0]
+    if pad and minval is None:
+        limits[0] -= span * pad
+    if pad and maxval is None:
+        limits[1] += span * pad
+    return ax.set_xlim(limits)
+
+def ylimits(ax, signal, minval=None, maxval=None, pad=0.05):
+    limits = [minval, maxval]
+    if minval is None:
+        limits[0] = signal.min()
+    if maxval is None:
+        limits[1] = signal.max()
+    span = limits[1] - limits[0]
+    if pad and minval is None:
+        limits[0] -= span * pad
+    if pad and maxval is None:
+        limits[1] += span * pad
+    return ax.set_ylim(limits)
+
+def xlabel(ax, label, y=-0.1, fontsize=20, **kwargs):
+    ax.set_xlabel(label, fontsize=fontsize, **kwargs)
+    ax.xaxis.set_label_coords(0.5, y)
+    return None
+
+def ylabel(ax, label, x=-0.2, fontsize=20, **kwargs):
+    ax.set_ylabel(label, fontsize=fontsize, **kwargs)
+    ax.yaxis.set_label_coords(x, 0.5)
+    return None
+
+def super_xlabel(label, fig, high_ax, low_ax, y=0.005, **kwargs):
+    x = (low_ax.get_position().x0 + high_ax.get_position().x1) / 2
+    fig.supxlabel(label, x=x, y=y, **kwargs)
+    return None
+
+def super_ylabel(label, fig, high_ax, low_ax, x=0.005, **kwargs):
+    y = (low_ax.get_position().y0 + high_ax.get_position().y1) / 2
+    fig.supylabel(label, x=x, y=y, **kwargs)
+    return None
+
+def plot_line(ax, time, signal, ymin=None, ymax=None, xmin=None, xmax=None,
+              xpad=None, ypad=0.05, yloc=None, xloc=None, **kwargs):
+    handles = ax.plot(time, signal, **kwargs)
+    xlimits(ax, time, minval=xmin, maxval=xmax, pad=xpad)
+    ylimits(ax, signal, minval=ymin, maxval=ymax, pad=ypad)
+    if xloc is not None:
+        ax.xaxis.set_major_locator(plt.MultipleLocator(xloc))
+    if yloc is not None:
+        ax.yaxis.set_major_locator(plt.MultipleLocator(yloc))
+    return handles
+
+def plot_barcode(ax, time, binary, offset=0.5, xmin=None, xmax=None, **kwargs):
+    lower, upper, handles = 0, 1, []
+    for i in range(binary.shape[1]):
+        h = ax.fill_between(time, lower, upper, where=binary[:, i], **kwargs)
+        handles.append(h)
+        if i < binary.shape[1] - 1:
+            lower += offset + 1
+            upper += offset + 1
+    xlimits(ax, time, minval=xmin, maxval=xmax, pad=0)
+    ax.set_ylim(0, upper)
+    hide_axis(ax, 'bottom')
+    hide_axis(ax, 'left')
+    return handles
+
+def indicate_zoom(fig, high_ax, low_ax, zoom_abs, **kwargs):
+    y0 = low_ax.get_position().y0
+    y1 = high_ax.get_position().y1
+    transform = low_ax.transData + fig.transFigure.inverted()
+    x0 = transform.transform((zoom_abs[0], 0))[0]
+    x1 = transform.transform((zoom_abs[1], 0))[0]
+    fig.add_artist(plt.Rectangle((x0, y0), x1 - x0, y1 - y0,
+                                 transform=fig.transFigure, **kwargs))
+    return None
+
+def assign_colors(handles, types, colors):
+    for handle, type_id in zip(handles, types):
+        handle.set_color(colors[str(int(type_id))])
+    return None
+
+def reorder_traces(handles, signal, zlow=2, zhigh=2.5):
+    inds = np.argsort(signal.std(axis=0))
+    zorders = np.linspace(zlow, zhigh, len(inds))[::-1]
+    for ind, z in zip(inds, zorders):
+        handles[ind].set_zorder(z)
+    return None
+