def get_colors(adata, c):
if is_color_like(c):
return c
else:
if c+'_colors' not in adata.uns.keys():
palette = default_palette(None)
palette = adjust_palette(palette, length=len(adata.obs[c].cat.categories))
adata.uns[c + '_colors'] = palette[:len(adata.obs[c].cat.categories)].by_key()['color']
cluster_ix = adata.obs[c].cat.codes
return np.array([adata.uns[c + '_colors'][cluster_ix[i]] for i in range(adata.n_obs)])
def hist(arrays,
alpha=.5,
bins=None,
colors=None,
labels=None,
xlabel=None,
ylabel=None,
ax=None,
figsize=None,
dpi=None):
ax = pl.figure(None, figsize, dpi=dpi) if ax is None else ax
arrays = arrays if isinstance(arrays, (list, tuple)) else [arrays]
palette = default_palette(None)[::3][:len(arrays)].by_key()['color']
colors = palette if colors is None or len(colors) < len(arrays) else colors
for i, array in enumerate(arrays):
pl.hist(array[np.isfinite(array)],
bins=bins,
alpha=alpha,
color=colors[i],
label=labels[i] if labels is not None else None)
pl.legend()
pl.xlabel(xlabel if xlabel is not None else '')
pl.ylabel(ylabel if xlabel is not None else '')
pl.show()
# def phase(adata, var=None, x=None, y=None, color='louvain', fits='all', xlabel='spliced', ylabel='unspliced',
# fontsize=None, show=True, ax=None, **kwargs):
# if isinstance(var, str) and (var in adata.var_names):
# if (x is None) or (y is None):
# ix = np.where(adata.var_names == var)[0][0]
# x, y = adata.layers['Ms'][:, ix], adata.layers['Mu'][:, ix]
# else:
# ValueError('var not found in adata.var_names.')
#
# ax = scatter(adata, x=x, y=y, color=color, frameon=True, title=var, xlabel=xlabel, ylabel=ylabel, ax=ax, **kwargs)
#
# xnew = np.linspace(0, x.max() * 1.02)
# fits = adata.layers.keys() if fits == 'all' else fits
# fits = [fit for fit in fits if 'velocity' in fit]
# for fit in fits:
# linestyle = '--' if 'stochastic' in fit else '-'
# pl.plot(xnew, adata.var[fit+'_gamma'][ix] / adata.var[fit+'_beta'][ix] * xnew
# + adata.var[fit+'_offset'][ix] / adata.var[fit+'_beta'][ix], c='k', linestyle=linestyle)
#
# if show: pl.show()
# else: return ax
def set_rcParams_scvelo(fontsize=8, color_map=None):
"""Set matplotlib.rcParams to scvelo defaults."""
# dpi options (mpl default: 100, 100)
rcParams['figure.dpi'] = 100
rcParams['savefig.dpi'] = 150
# figure (mpl default: 0.125, 0.96, 0.15, 0.91)
rcParams['figure.figsize'] = (7, 5)
rcParams['figure.subplot.left'] = 0.18
rcParams['figure.subplot.right'] = 0.96
rcParams['figure.subplot.bottom'] = 0.15
rcParams['figure.subplot.top'] = 0.91
# lines (defaults: 1.5, 6, 1)
rcParams['lines.linewidth'] = 1.5 # the line width of the frame
rcParams['lines.markersize'] = 6
rcParams['lines.markeredgewidth'] = 1
# font
rcParams['font.sans-serif'] = \
['Arial', 'Helvetica', 'DejaVu Sans',
'Bitstream Vera Sans', 'sans-serif']
fontsize = fontsize
labelsize = 0.9 * fontsize
# fonsizes (mpl default: 10, medium, large, medium)
rcParams['font.size'] = fontsize
rcParams['legend.fontsize'] = labelsize
rcParams['axes.titlesize'] = fontsize
rcParams['axes.labelsize'] = labelsize
# legend (mpl default: 1, 1, 2, 0.8)
rcParams['legend.numpoints'] = 1
rcParams['legend.scatterpoints'] = 1
rcParams['legend.handlelength'] = 0.5
rcParams['legend.handletextpad'] = 0.4
# color cycle
rcParams['axes.prop_cycle'] = default_palette()
# axes
rcParams['axes.linewidth'] = 0.8
rcParams['axes.edgecolor'] = 'black'
rcParams['axes.facecolor'] = 'white'
# ticks (mpl default: k, k, medium, medium)
rcParams['xtick.color'] = 'k'
rcParams['ytick.color'] = 'k'
rcParams['xtick.labelsize'] = labelsize
rcParams['ytick.labelsize'] = labelsize
# axes grid (mpl default: False, #b0b0b0)
rcParams['axes.grid'] = False
rcParams['grid.color'] = '.8'
# color map
rcParams['image.cmap'] = rcParams[
'image.cmap'] if color_map is None else color_map
# frame (mpl default: True)
global _frameon
_frameon = False