def plotTTPMat(ax: axes,
toa: np.array,
ttp: np.array,
title: str = None,
plot_ylabel: bool = False) -> None:
ax.scatter(toa, ttp, marker='o', c=ttp, alpha=0.75)
ax.set_ylim(PRI_DETECTED_RANGE[0], PRI_DETECTED_RANGE[1])
ax.xaxis.get_major_formatter().set_powerlimits((0, 1))
ax.set_title(title, fontsize=10)
ax.set_xlabel('toa[us]', fontsize=8, loc='right')
if plot_ylabel:
ax.set_ylabel('pri[us]', fontsize=9)
def cohort_bar(cohort_averages: dict,
cohort_data: dict,
observable: str,
yaxis_upper: int = None,
ax: matplotlib.axes = None,
labelsize: int = 12,
ticksize: int = 10,
legendsize: int = 8,
markersize=15) -> None:
"""Plots either the V- or J-gene usages.
Parameters
----------
cohort_averages : dict
Dictionary of averages and variations within a cohort for all severities.
cohort_dict : dict
Dictionary of all statistics of all individuals in a cohort for all severities.
observable : str
The quantity which is going to be plotted.
yaxis_upper : int, optional
Specifies the upper limit of the y-axis on the plot.
ax : matplotlib.axes, optional
Used to modify an already existing axes when creating a figure with a grid.
labelsize : int, optional
Size of axes labels.
ticksize : int, optional
Size of tick labels.
legendsize : int, optional
Specifies font size of strings in legend.
Returns
-------
None
"""
if ax is None:
fig = plt.figure(dpi=300, figsize=(16, 4))
ax = fig.add_subplot(111)
# Give the bars for each gene some space among each other.
width = 1.0 / len(cohort_averages) - 0.02
bars = []
if 'Asymptomatic' in cohort_averages:
ordering = ['Healthy', 'Mild', 'Moderate', 'Severe', 'Asymptomatic']
else:
ordering = sorted(cohort_averages.keys())
# Sort the genes by descending usage in the healthy cohort.
if 'Briney/GRP' in cohort_averages:
sorted_genes = [
gene for _, gene in sorted(zip(
cohort_averages['Briney/GRP'][observable][0],
cohort_averages['Briney/GRP'][observable][-1]),
key=lambda pair: pair[0],
reverse=True)
]
else:
sorted_genes = [
gene for _, gene in sorted(zip(
cohort_averages['Healthy'][observable][0],
cohort_averages['Healthy'][observable][-1]),
key=lambda pair: pair[0],
reverse=True)
]
# Because there are so many V genes, plot only those which have at least
# 1% average usage in at least one cohort.
if 'v' in observable:
good_genes = []
for gene in sorted_genes:
bools = 0
for severity in cohort_averages:
idx = cohort_averages[severity][observable][-1].index(gene)
value = cohort_averages[severity][observable][0][idx]
bools += value >= 0.01
if bools != 0:
good_genes.append(gene)
else:
good_genes = sorted_genes
xlabels = good_genes
default_x = np.arange(0, len(good_genes), 1)
xs, ys = [], []
for i, severity in enumerate(ordering):
x = default_x + width * i
xs.append(x)
indices = [
cohort_averages[severity][observable][-1].index(gene)
for gene in good_genes
]
y = [cohort_averages[severity][observable][0][k] for k in indices]
ys.append(y)
if observable == 'v gene':
ax.set_xlim(-0.3, xs[0][-1] + 1.0)
if yaxis_upper is not None:
ax.set_ylim(0, yaxis_upper)
else:
ax.set_ylim(0, 0.35)
else:
ax.set_xlim(-0.3, xs[0][-1] + 1.0)
if yaxis_upper is not None:
ax.set_ylim(0, yaxis_upper)
else:
ax.set_ylim(0, 0.55)
# Specifiy location of xticks as being in the middle of the grouping of bars.
middle = np.mean(np.arange(0, len(cohort_averages)))
middle_xticks = default_x + middle * width
ax.set_xticks(middle_xticks)
ax.set_xticklabels(xlabels, rotation=90, family='Arial')
ax.set_ylabel('relative counts', fontname="Arial")
# Plot the bars.
for i, severity in enumerate(ordering):
bar = ax.bar(xs[i],
ys[i],
width,
color=colors[severity],
label=severity)
for d in cohort_data[severity][observable]:
# Plot the full distributions of values to get a better sense
# of variation within cohorts.
for gidx, rect in enumerate(bar):
ax.scatter(xs[i][gidx],
d[good_genes[gidx]],
marker='.',
color=lightercolors[severity],
zorder=3,
s=markersize,
edgecolors='black',
linewidths=0.3)
format_axes(ax,
labelsize=labelsize,
ticksize=ticksize,
legendsize=legendsize)
