code stringlengths 3 6.57k |
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sub_array(maxy, i) |
addEnds(x, _miny) |
addEnds(x, _maxy) |
polys.append(poly) |
sub_array(dy, i) |
addEnds(x, _dy) |
polys.append(poly) |
ax.margins(x=0) |
callable(ticklabels) |
ax.get_xaxis() |
set_major_formatter(ticker.FuncFormatter(ticklabels) |
ax.get_xaxis() |
set_major_formatter(ticker.IndexFormatter(ticklabels) |
ax.xaxis.set_major_locator(ticker.AutoLocator() |
ax.xaxis.set_minor_locator(ticker.AutoMinorLocator() |
showMatrix(matrix, x_array=None, y_array=None, **kwargs) |
kwargs.pop('percentile', None) |
np.percentile(matrix, p) |
np.percentile(matrix, 100-p) |
kwargs.pop('vmin', vmin) |
kwargs.pop('vmax', vmax) |
kwargs.pop('vcenter', None) |
kwargs.pop('norm', None) |
DivergingNorm(vmin=vmin, vcenter=0., vmax=vmax) |
LOGGER.warn('vcenter cannot be used in Python 2 so norm remains None') |
kwargs.pop('linewidth', 1) |
kwargs.pop('ratio', 6) |
kwargs.pop('ticklabels', None) |
kwargs.pop('xticklabels', ticklabels) |
kwargs.pop('yticklabels', ticklabels) |
kwargs.pop('xtickrotation', 0.) |
kwargs.pop('colorbar', True) |
kwargs.pop('cb_extend', 'neither') |
kwargs.pop('allticks', False) |
kwargs.pop('interactive', True) |
kwargs.pop('cmap', 'jet') |
kwargs.pop('origin', 'lower') |
isinstance(y_array, Phylo.BaseTree.Tree) |
isinstance(x_array, Phylo.BaseTree.Tree) |
kwargs.pop('aspect', None) |
subplot(gs[main_index]) |
gca() |
ax3.set_xlim([-0.5, matrix.shape[0]+0.5]) |
ax3.set_ylim([-0.5, matrix.shape[1]+0.5]) |
ax3.xaxis.set_major_formatter(ticker.IndexFormatter(xticklabels) |
ax3.yaxis.set_major_formatter(ticker.IndexFormatter(yticklabels) |
ax3.xaxis.set_major_locator(ticker.IndexLocator(offset=0.5, base=1.) |
ax3.yaxis.set_major_locator(ticker.IndexLocator(offset=0.5, base=1.) |
ticker.AutoLocator() |
locator.set_params(integer=True) |
ticker.AutoMinorLocator() |
ax3.xaxis.set_major_locator(locator) |
ax3.xaxis.set_minor_locator(minor_locator) |
ticker.AutoLocator() |
locator.set_params(integer=True) |
ticker.AutoMinorLocator() |
ax3.yaxis.set_major_locator(locator) |
ax3.yaxis.set_minor_locator(minor_locator) |
ax3.yaxis.set_major_formatter(ticker.NullFormatter() |
subplot(gs[upper_index]) |
min(Y.values() |
max(Y.values() |
min(X.values() |
max(X.values() |
ax1.set_xlim(minx-.5, maxx+.5) |
ax1.set_ylim(miny, 1.05*maxy) |
ax1.set_xticklabels([]) |
interpY(y) |
np.array([xp, yp]) |
T.reshape(-1, 1, 2) |
np.concatenate([points[:-1], points[1:]], axis=1) |
LineCollection(segments, array=yp, linewidths=lw, cmap=cmap) |
lines.append(lcy) |
ax1.add_collection(lcy) |
ax1.set_xlim(xp.min() |
xp.max() |
ax1.set_ylim(yp.min() |
yp.max() |
ax3.xaxis_inverted() |
ax2.invert_xaxis() |
ax1.axis('off') |
subplot(gs[left_index]) |
drawTree(y_array, label_func=None, inverted=True) |
min(Y.values() |
max(Y.values() |
min(X.values() |
max(X.values() |
ax2.set_ylim(miny-.5, maxy+.5) |
ax2.set_xlim(minx, 1.05*maxx) |
ax2.set_xticklabels([]) |
interpY(y) |
np.array([yp, xp]) |
T.reshape(-1, 1, 2) |
np.concatenate([points[:-1], points[1:]], axis=1) |
LineCollection(segments, array=yp, linewidths=lw, cmap=cmap) |
lines.append(lcx) |
ax2.add_collection(lcx) |
ax2.set_xlim(yp.min() |
yp.max() |
ax2.set_ylim(xp.min() |
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