def plot_graphs(cell_line, lineage_num, num_plots=5, parA_heatmap=None, save=True, labels=None, um=False, plot_kwargs=None):
lineage = track.Lineage()
if save:
fig = plt.figure(figsize=(20, 10))
gs = matplotlib.gridspec.GridSpec(2, 3)
fig.patch.set_alpha(0)
spots_ParA = []
traces_ParA = []
L = []
T = shared.get_timings()
for cell in cell_line:
spots_ParA.append(cell.ParA)
traces_ParA.append(cell.parA_fluorescence_smoothed[::-1])
if um:
L.append(cell.length[0][0] * PX)
else:
L.append(cell.length[0][0])
L = np.array(L)
traces_ParA = np.concatenate(traces_ParA)
max_parA_intensity = traces_ParA.max()
start = cell_line[0].frame - 1
end = cell_line[-1].frame - 1
t = np.array(T[start:end + 1])
if save:
parA_heatmap = fig.add_subplot(gs[0, 0])
_despine(parA_heatmap)
# use Rectangles to generate a heatmap
i = 0
cmapper = plt.cm.get_cmap("afmhot")
for cell in cell_line:
trace = cell.parA_fluorescence_smoothed
if um:
l = cell.length[0][0] * PX
else:
l = cell.length[0][0]
x0 = t[i] - 8
y0 = -(l / 2)
increment = l / len(trace)
colours = cmapper(trace / max_parA_intensity)
i2 = 0
for _t in trace:
if _t < 0:
_t = 0
r = matplotlib.patches.Rectangle(
(x0, y0),
width=15,
height=increment,
facecolor=colours[i2],
edgecolor="none",
)
parA_heatmap.add_patch(r)
y0 += increment
i2 += 1
i += 1
if save:
parA_heatmap.set_ylabel(r"Distance from mid-cell (px)")
parA_heatmap.set_xlabel(r"Time (min)")
parA_heatmap.set_title("ParA")
poledict = poles.PoleAssign(lineage.frames).assign_poles()
if poledict[cell_line[0].id] is None:
parA_heatmap.plot(t, L / 2, "r-", lw=2)
parA_heatmap.plot(t, -(L / 2), "r-", lw=2)
else:
parA_heatmap.plot(t, L / 2, "k-", lw=2)
parA_heatmap.plot(t, -(L / 2), "k-", lw=2)
parAs = {}
i = 0
for s in spots_ParA:
midcell = s[2] / 2
spot = s[0] - midcell
parAs[t[i]] = spot
i += 1
parAs = np.array(sorted(parAs.items()))
if num_plots >= 2:
parA_heatmap.plot(
parAs[:, 0], parAs[:, 1],
lw=2, marker=".", mec="k", ms=10
)
decorate_daughters(cell_line, lineage, parA_heatmap, labels=labels, um=um)
parA_heatmap.patch.set_alpha(0)
if num_plots >= 3:
ax_parA = fig.add_subplot(gs[1, 0])
_despine(ax_parA)
ax_parA.set_title("ParA maximum")
ax_parA.plot(
parAs[:, 0], (L / 2) - parAs[:, 1],
marker=".", lw=2, mec="k", ms=10,
label="Distance from top pole"
)
ax_parA.plot(
parAs[:, 0], (L / 2) + parAs[:, 1],
marker=".", lw=2, mec="k", ms=10,
label="Distance from bottom pole"
)
ax_parA.set_xlabel(r"Time (min)")
ax_parA.set_ylabel(r"Distance (px)")
ax_parA.patch.set_alpha(0)
if num_plots >= 2:
parB_midcell = fig.add_subplot(gs[0, 1])
_despine(parB_midcell)
parB_midcell.set_title("ParB")
parB_midcell.plot(t, L / 2, "k-", lw=2, label="Cell poles")
parB_midcell.plot(t, -(L / 2), "k-", lw=2)
spots_ParB = shared.get_parB_path(cell_line, T, lineage_num)
spotnum = 1
for x in spots_ParB:
s = x.spots(False)
if hasattr(x, "split_parent") and x.split_parent:
for y in spots_ParB:
if y.spot_ids[-1] == x.split_parent:
textra = y.timing[-1:]
timings = np.concatenate([textra, s["timing"]])
posextra = np.array(y.position[-1:])
if um:
positions = np.concatenate([posextra * PX, s["position"] * PX])
else:
positions = np.concatenate([posextra, s["position"]])
break
else:
timings = s["timing"]
if um:
positions = s["position"] * PX
else:
positions = s["position"]
if num_plots >= 2:
ax_target = parB_midcell
label = "Spot {0}".format(spotnum)
else:
ax_target = parA_heatmap
label = "ParB"
if plot_kwargs:
ax_target.plot(
timings, positions, **plot_kwargs
)
else:
# ax_target.plot(
# timings, positions,
# lw=2,
# marker=".",
# markeredgecolor="k",
# ms=10,
# label=label,
# color=colour,
# )
ax_target.plot(
timings, positions,
lw=2,
marker=".",
markeredgecolor="k",
ms=10,
label=label,
color="k",
path_effects=[
matplotlib.patheffects.Stroke(
linewidth=2, foreground=(0.7, 0.7, 0.7)
)
],
)
dparA = []
for spot in s:
parApos = parAs[np.where(parAs[:, 0] == spot[0])][0, 1]
dpA = spot[1] - parApos
dparA.append(dpA)
x.parA_d = dparA
x.parA_dmean = np.mean(dparA)
x.parA_dsem = np.std(dparA) / np.sqrt(len(dparA))
x.spotnum = spotnum
x.intensity_mean = s["intensity"].mean()
spotnum += 1
if num_plots >= 2:
lines = parB_midcell.lines[::-1]
for l in lines:
parB_midcell.lines.remove(l)
parB_midcell.add_line(l)
parB_midcell.set_ylabel(r"Distance from mid-cell (px)")
parB_midcell.set_xlabel(r"Time (min)")
decorate_daughters(cell_line, lineage, parB_midcell, pad=5, labels=labels, um=um)
parB_midcell.legend(bbox_to_anchor=(1.35, 1))
parB_midcell.patch.set_alpha(0)
else:
if save:
parA_heatmap.legend(
[parA_heatmap.lines[-1]], [parA_heatmap.lines[-1].get_label()],
bbox_to_anchor=(1.2, 1)
)
if num_plots >= 4:
filtered = [x for x in spots_ParB if len(x) > 4]
if len(filtered) > 0:
ax_parB_closest = fig.add_subplot(gs[1, 1], sharex=ax_parA, sharey=ax_parA)
dmin = min(
filtered,
key=lambda x: np.abs(x.parA_dmean)
)
ax_parB_closest.set_title("ParB spot {0} (dmin)".format(dmin.spotnum))
_despine(ax_parB_closest)
s = dmin.spots(False)
dpol_t = (dmin.len() / 2) - s["position"]
dpol_b = (dmin.len() / 2) + s["position"]
ax_parB_closest.plot(
s["timing"], dpol_t,
marker=".", lw=2, mec="k", ms=10,
label="Distance from top pole"
)
ax_parB_closest.plot(
s["timing"], dpol_b,
marker=".", lw=2, mec="k", ms=10,
label="Distance from bottom pole"
)
ax_parB_closest.plot(
s["timing"], dmin.parA_d,
marker=".", lw=2, ms=10,
label="Distance from ParA focus"
)
ax_parB_closest.plot(
ax_parB_closest.get_xlim(),
[0, 0],
"k--"
)
ax_parB_closest.patch.set_alpha(0)
if num_plots >= 5:
imax = max(filtered, key=lambda x: x.intensity_mean)
if imax.id != dmin.id:
ax_parB_highest = fig.add_subplot(gs[1, 2], sharex=ax_parB_closest, sharey=ax_parA)
s = imax.spots(False)
dpol_t = (imax.len() / 2) - s["position"]
dpol_b = (imax.len() / 2) + s["position"]
ax_parB_highest.plot(s["timing"], dpol_t, marker=".", lw=2, mec="k", ms=10, label="Distance from top pole")
ax_parB_highest.plot(s["timing"], dpol_b, marker=".", lw=2, mec="k", ms=10, label="Distance from bottom pole")
ax_parB_highest.plot(s["timing"], imax.parA_d, marker=".", lw=2, mec="k", ms=10, label="Distance from ParA focus")
ax_parB_highest.plot(ax_parB_highest.get_xlim(), [0, 0], "k--")
_despine(ax_parB_highest)
ax_parB_highest.set_title("ParB Spot {0} (imax)".format(imax.spotnum))
ax_parB_highest.set_ylabel(r"Distance (px)")
ax_parB_highest.set_xlabel("Time (min)")
ax_parB_highest.patch.set_alpha(0)
ax_parB_highest.legend(bbox_to_anchor=(0.8, 1.35))
else:
ax_parB_closest.legend(bbox_to_anchor=(1.65, 1))
else:
ax_parB_closest.legend(bbox_to_anchor=(1.65, 1))
else:
ax_parA.legend(bbox_to_anchor=(1.65, 1))
if save:
plt.tight_layout()
fn = "data/data-lineage{0:02d}.pdf".format(lineage_num)
plt.savefig(fn)
print("Saved data file to {0}".format(fn))
def plot_graphs_parB_only(cell_line, lineage_num, ax_parB=None, save=True, labels=None, um=False):
if um:
L = np.array([x.length[0][0] * PX for x in cell_line])
else:
L = np.array([x.length[0][0] for x in cell_line])
T = shared.get_timings()
t = np.array(T[cell_line[0].frame - 1:cell_line[-1].frame])
lineage = track.Lineage()
if not ax_parB:
fig = plt.figure(figsize=(20 / 3, 5))
ax_parB = fig.add_subplot(111)
_despine(ax_parB)
ax_parB.set_title("ParB")
ax_parB.set_ylabel(r"Distance from mid-cell (px)")
ax_parB.set_xlabel(r"Time (min)")
poledict = poles.PoleAssign(lineage.frames).assign_poles()
if poledict[cell_line[0].id] is None:
ax_parB.plot(t, L / 2, "r-", lw=2, label="Cell poles")
ax_parB.plot(t, -(L / 2), "r-", lw=2)
else:
ax_parB.plot(t, L / 2, "k-", lw=2, label="Cell poles")
ax_parB.plot(t, -(L / 2), "k-", lw=2)
spots_ParB = shared.get_parB_path(cell_line, T, lineage_num)
spotnum = 1
colourwheel = sns.color_palette(n_colors=len(spots_ParB))
for x in spots_ParB:
colour = colourwheel[spotnum - 1]
s = x.spots(False)
if hasattr(x, "split_parent") and x.split_parent:
for y in spots_ParB:
if y.spot_ids[-1] == x.split_parent:
textra = y.timing[-1:]
timings = np.concatenate([textra, s["timing"]])
posextra = np.array(y.position[-1:])
if um:
positions = np.concatenate([posextra * PX, s["position"] * PX])
else:
positions = np.concatenate([posextra, s["position"]])
break
else:
timings = s["timing"]
if um:
positions = s["position"] * PX
else:
positions = s["position"]
ax_parB.plot(
timings, positions,
lw=2, marker=".",
mec="k", ms=10,
label="Spot {0}".format(spotnum),
color=colour
)
spotnum += 1
lines = ax_parB.lines[::-1]
for l in lines:
ax_parB.lines.remove(l)
ax_parB.add_line(l)
decorate_daughters(cell_line, lineage, ax_parB, pad=5, labels=labels, um=um)
if save:
ax_parB.legend(bbox_to_anchor=(1.35, 1))
ax_parB.patch.set_alpha(0)
plt.tight_layout()
fn = "data/data-lineage{0:02d}.pdf".format(lineage_num)
plt.savefig(fn)
print("Saved data file to {0}".format(fn))
plt.close()