def plot_knn(ds: loompy.LoomConnection, out_file: str) -> None:
n_cells = ds.shape[1]
valid = ds.col_attrs["_Valid"].astype('bool')
(a, b, w) = ds.get_edges("MKNN", axis=1)
mknn = sparse.coo_matrix(
(w, (a, b)), shape=(n_cells, n_cells)).tocsr()[valid, :][:, valid]
xy = np.vstack(
(ds.col_attrs["_X"], ds.col_attrs["_Y"])).transpose()[valid, :]
fig = plt.figure(figsize=(10, 10))
g = nx.from_scipy_sparse_matrix(mknn)
ax = fig.add_subplot(111)
nx.draw_networkx_edges(g, pos=xy, alpha=0.25, width=0.2, edge_color='gray')
ax.axis('off')
plt.tight_layout()
fig.savefig(out_file, format="png", dpi=300)
plt.close()
def plot_graph(ds: loompy.LoomConnection,
out_file: str,
tags: List[str] = None) -> None:
logging.info("Loading graph")
n_cells = ds.shape[1]
cells = np.where(ds.col_attrs["_Valid"] == 1)[0]
has_edges = False
if "MKNN" in ds.list_edges(axis=1):
(a, b, w) = ds.get_edges("MKNN", axis=1)
has_edges = True
pos = np.vstack((ds.col_attrs["_X"], ds.col_attrs["_Y"])).transpose()
labels = ds.col_attrs["Clusters"]
if "Outliers" in ds.col_attrs:
outliers = ds.col_attrs["Outliers"]
else:
outliers = np.zeros(ds.shape[1])
# Compute a good size for the markers, based on local density
logging.info("Computing node size")
min_pts = 50
eps_pct = 60
nn = NearestNeighbors(n_neighbors=min_pts, algorithm="ball_tree", n_jobs=4)
nn.fit(pos)
knn = nn.kneighbors_graph(mode='distance')
k_radius = knn.max(axis=1).toarray()
epsilon = 24 * np.percentile(k_radius, eps_pct)
fig = plt.figure(figsize=(10, 10))
ax = fig.add_subplot(111)
# Draw edges
if has_edges:
logging.info("Drawing edges")
lc = LineCollection(zip(pos[a], pos[b]),
linewidths=0.25,
zorder=0,
color='grey',
alpha=0.1)
ax.add_collection(lc)
# Draw nodes
logging.info("Drawing nodes")
colors20 = np.vstack((plt.cm.Vega20b(np.linspace(0., 1, 20))[::2],
plt.cm.Vega20c(np.linspace(0, 1, 20))[1::2]))
plots = []
names = []
for i in range(max(labels) + 1):
cluster = labels == i
n_cells = cluster.sum()
if np.all(outliers[labels == i] == 1):
edgecolor = colorConverter.to_rgba('red', alpha=.1)
plots.append(
plt.scatter(x=pos[outliers == 1, 0],
y=pos[outliers == 1, 1],
c='grey',
marker='.',
edgecolors=edgecolor,
alpha=0.1,
s=epsilon))
names.append(f"{i}/n={n_cells} (outliers)")
else:
plots.append(
plt.scatter(x=pos[cluster, 0],
y=pos[cluster, 1],
c=cg.colors75[np.mod(i, 75)],
marker='.',
lw=0,
s=epsilon,
alpha=0.75))
txt = str(i)
if "ClusterName" in ds.ca.keys():
txt = ds.ca.ClusterName[ds.ca.Clusters == i][0]
if tags is not None:
names.append(f"{txt}/n={n_cells} " +
tags[i].replace("\n", " "))
else:
names.append(f"{txt}/n={n_cells}")
logging.info("Drawing legend")
plt.legend(plots,
names,
scatterpoints=1,
markerscale=2,
loc='upper left',
bbox_to_anchor=(1, 1),
fancybox=True,
framealpha=0.5,
fontsize=10)
logging.info("Drawing cluster IDs")
for lbl in range(0, max(labels) + 1):
txt = str(lbl)
if "ClusterName" in ds.ca.keys():
txt = ds.ca.ClusterName[ds.ca.Clusters == lbl][0]
if np.all(outliers[labels == lbl] == 1):
continue
if np.sum(labels == lbl) == 0:
continue
(x, y) = np.median(pos[np.where(labels == lbl)[0]], axis=0)
ax.text(x,
y,
txt,
fontsize=12,
bbox=dict(facecolor='white', alpha=0.5, ec='none'))
logging.info("Saving to file")
fig.savefig(out_file, format="png", dpi=144, bbox_inches='tight')
plt.close()
def plot_graph_age(ds: loompy.LoomConnection, out_file: str,
tags: List[str]) -> None:
def parse_age(age: str) -> float:
if age == "":
return 0
unit, amount = age[0], float(age[1:])
if unit == "P":
amount += 19.
return amount
n_cells = ds.shape[1]
valid = ds.col_attrs["_Valid"].astype('bool')
(a, b, w) = ds.get_edges("MKNN", axis=1)
mknn = sparse.coo_matrix(
(w, (a, b)), shape=(n_cells, n_cells)).tocsr()[valid, :][:, valid]
sfdp = np.vstack(
(ds.col_attrs["_X"], ds.col_attrs["_Y"])).transpose()[valid, :]
# The sorting below is to make every circle visible and avoid overlappings in crowded situations
orderx = np.argsort(sfdp[:, 0], kind="mergesort")
ordery = np.argsort(sfdp[:, 1], kind="mergesort")
orderfin = orderx[ordery]
sfdp_original = sfdp.copy(
) # still the draw_networkx_edges wants the sfd with respect of the graph `g`
# \it is shortcut to avoid resorting the graph
sfdp = sfdp[orderfin, :]
labels = ds.col_attrs["Clusters"][valid][orderfin]
age = np.fromiter(map(parse_age, ds.col_attrs["Age"]),
dtype=float)[valid][orderfin]
fig = plt.figure(figsize=(10, 10))
g = nx.from_scipy_sparse_matrix(mknn)
ax = fig.add_subplot(111)
# Draw the KNN graph first, with gray transparent edges
nx.draw_networkx_edges(g,
pos=sfdp_original,
alpha=0.1,
width=0.1,
edge_color='gray')
# Then draw the nodes, colored by label
block_colors = plt.cm.nipy_spectral_r((age - 6) / 14.)
nx.draw_networkx_nodes(g,
pos=sfdp,
node_color=block_colors,
node_size=10,
alpha=0.4,
linewidths=0)
for lbl in range(0, max(labels) + 1):
if np.sum(labels == lbl) == 0:
continue
(x, y) = np.median(sfdp[np.where(labels == lbl)[0]], axis=0)
text = "#" + str(lbl)
if len(tags[lbl]) > 0:
text += "\n" + tags[lbl]
ax.text(x,
y,
text,
fontsize=8,
bbox=dict(facecolor='gray', alpha=0.3, ec='none'))
ax.axis('off')
levels = np.unique(age)
for il, lev in enumerate(levels):
ax.add_patch(
plt.Rectangle((0.90, 0.7 + il * 0.016),
0.014,
0.014,
color=plt.cm.nipy_spectral_r((lev - 6) / 14.),
clip_on=0,
transform=ax.transAxes))
ax.text(0.93,
0.703 + il * 0.016,
("E%.1f" % lev if lev < 18.5 else "P%.1f" % (lev - 19)),
transform=ax.transAxes)
plt.tight_layout()
fig.savefig(out_file, format="png", dpi=300)
plt.close()
def plot_classification(ds: loompy.LoomConnection, out_file: str) -> None:
n_cells = ds.shape[1]
valid = ds.col_attrs["_Valid"].astype('bool')
(a, b, w) = ds.get_edges("MKNN", axis=1)
mknn = sparse.coo_matrix(
(w, (a, b)), shape=(n_cells, n_cells)).tocsr()[valid, :][:, valid]
pos = np.vstack(
(ds.col_attrs["_X"], ds.col_attrs["_Y"])).transpose()[valid, :]
labels = ds.col_attrs["Clusters"][valid]
fig = plt.figure(figsize=(10, 10))
g = nx.from_scipy_sparse_matrix(mknn)
classes = [
"Neurons", "Astrocyte", "Ependymal", "OEC", "Oligos", "Schwann",
"Cycling", "Vascular", "Immune"
]
colors = [plt.cm.get_cmap('Vega20')((ix + 0.5) / 20) for ix in range(20)]
combined_colors = np.zeros((ds.shape[1], 4)) + np.array((0.5, 0.5, 0.5, 0))
for ix, cls in enumerate(classes):
cmap = LinearSegmentedColormap.from_list('custom cmap',
[(1, 1, 1, 0), colors[ix]])
cells = ds.col_attrs["Class0"] == classes[ix]
if np.sum(cells) > 0:
combined_colors[cells] = [
cmap(x) for x in ds.col_attrs["Class_" + classes[ix]][cells]
]
cmap = LinearSegmentedColormap.from_list('custom cmap',
[(1, 1, 1, 0), colors[ix + 1]])
ery_color = np.array(
[[1, 1, 1, 0],
[0.9, 0.71, 0.76,
0]])[(ds.col_attrs["Class"][valid] == "Erythrocyte").astype('int')]
cells = ds.col_attrs["Class0"] == "Erythrocyte"
if np.sum(cells) > 0:
combined_colors[cells] = np.array([1, 0.71, 0.76, 0])
cmap = LinearSegmentedColormap.from_list('custom cmap',
[(1, 1, 1, 0), colors[ix + 2]])
exc_color = np.array(
[[1, 1, 1, 0],
[0.5, 0.5, 0.5,
0]])[(ds.col_attrs["Class0"][valid] == "Excluded").astype('int')]
cells = ds.col_attrs["Class0"] == "Excluded"
if np.sum(cells) > 0:
combined_colors[cells] = np.array([0.5, 0.5, 0.5, 0])
ax = fig.add_subplot(1, 1, 1)
ax.set_title("Class")
nx.draw_networkx_edges(g, pos=pos, alpha=0.2, width=0.1, edge_color='gray')
nx.draw_networkx_nodes(g,
pos=pos,
node_color=combined_colors[valid],
node_size=10,
alpha=0.6,
linewidths=0)
ax.axis('off')
plt.tight_layout()
fig.savefig(out_file, format="png", dpi=300)
plt.close()
def fit_predict(self, ds: loompy.LoomConnection) -> np.ndarray:
n_valid = np.sum(ds.col_attrs["_Valid"] == 1)
n_total = ds.shape[1]
logging.info("%d of %d cells were valid", n_valid, n_total)
logging.info("%d of %d genes were valid",
np.sum(ds.row_attrs["_Valid"] == 1), ds.shape[0])
cells = np.where(ds.col_attrs["_Valid"] == 1)[0]
if self.method == "hdbscan":
logging.info("HDBSCAN clustering in t-SNE space")
min_pts = 10 if n_valid < 3000 else (
20 if n_valid < 20000 else 100)
tsne_pos = np.vstack(
(ds.col_attrs["_X"], ds.col_attrs["_Y"])).transpose()[cells, :]
clusterer = hdbscan.HDBSCAN(min_cluster_size=min_pts)
labels = clusterer.fit_predict(tsne_pos)
elif self.method == "dbscan":
logging.info("DBSCAN clustering in t-SNE space")
if self.min_pts is None:
self.min_pts = 10 if n_valid < 3000 else (
20 if n_valid < 20000 else 100)
tsne_pos = np.vstack(
(ds.col_attrs["_X"], ds.col_attrs["_Y"])).transpose()[cells, :]
# Determine a good epsilon
nn = NearestNeighbors(n_neighbors=self.min_pts,
algorithm="ball_tree",
n_jobs=4)
nn.fit(tsne_pos)
knn = nn.kneighbors_graph(mode='distance')
k_radius = knn.max(axis=1).toarray()
epsilon = np.percentile(k_radius, self.eps_pct)
clusterer = DBSCAN(eps=epsilon, min_samples=self.min_pts)
labels = clusterer.fit_predict(tsne_pos)
if not self.outliers:
# Assign each outlier to the same cluster as the nearest non-outlier
nn = NearestNeighbors(n_neighbors=50, algorithm="ball_tree")
nn.fit(tsne_pos[labels >= 0])
nearest = nn.kneighbors(tsne_pos[labels == -1],
n_neighbors=1,
return_distance=False)
labels[labels == -1] = labels[labels >= 0][nearest.flat[:]]
elif self.method == "multilev":
logging.info(
"comunity-multilevel clustering on unweighted KNN graph")
(a, b, w) = ds.get_edges("KNN", axis=1)
# knn = sparse.coo_matrix((w, (a, b)), shape=(ds.shape[1], ds.shape[1])).tocsr()[cells, :][:, cells]
# sources, targets = knn.nonzero()
G = igraph.Graph(n_total, list(zip(a, b)), directed=False)
VxCl = G.community_multilevel(return_levels=False)
labels = np.array(VxCl.membership)
elif self.method == "wmultilev":
logging.info(
"comunity-multilevel clustering on the multiscale KNN graph")
(a, b, w) = ds.get_edges("KNN", axis=1)
# knn = sparse.coo_matrix((w, (a, b)), shape=(ds.shape[1], ds.shape[1])).tocsr()[cells, :][:, cells]
# a, b = knn.nonzero()
G = igraph.Graph(n_total,
list(zip(a, b)),
directed=False,
edge_attrs={'weight': w})
VxCl = G.community_multilevel(return_levels=False,
weights="weight")
labels = np.array(VxCl.membership)
elif self.method == "mknn_louvain":
logging.info(
"comunity-multilevel clustering on the multiscale MKNN graph")
(a, b, w) = ds.get_edges("MKNN", axis=1)
random.seed(13)
igraph._igraph.set_random_number_generator(random)
G = igraph.Graph(n_total,
list(zip(a, b)),
directed=False,
edge_attrs={'weight': w})
VxCl = G.community_multilevel(return_levels=False,
weights="weight")
labels = np.array(VxCl.membership)
logging.info(f"labels.shape = {labels.shape}")
if not self.outliers:
bigs = np.where(np.bincount(labels) >= 0)[0]
else:
bigs = np.where(np.bincount(labels) >= self.min_pts)[0]
mapping = {k: v for v, k in enumerate(bigs)}
labels = np.array(
[mapping[x] if x in bigs else -1 for x in labels])
else:
logging.info("Louvain clustering on the multiscale KNN graph")
(a, b, w) = ds.get_edges("KNN", axis=1)
knn = sparse.coo_matrix(
(w, (a, b)),
shape=(ds.shape[1], ds.shape[1])).tocsr()[cells, :][:, cells]
lj = cg.LouvainJaccard(resolution=1, jaccard=False)
labels = lj.fit_predict(knn.tocoo())
# At this point, cells should be labeled 0, 1, 2, ...
# But there may also be cells labelled -1 for outliers, which we want to keep track of
labels_all = np.zeros(ds.shape[1], dtype='int')
outliers = np.zeros(ds.shape[1], dtype='int')
labels_all[cells] = labels
outliers[labels_all == -1] = 1
labels_all[cells] = labels - np.min(labels)
ds.ca.Clusters = labels_all
ds.ca.Outliers = outliers
logging.info("Found " + str(max(labels_all) + 1) + " clusters")
if not len(set(ds.ca.Clusters)) == ds.ca.Clusters.max() + 1:
raise ValueError("There are holes in the cluster ID sequence!")
return labels_all
