def compute_ari(idx, param_df, classes, class_type="Class 1", remove_non_mb=False):
preprocess_params = dict(param_df.loc[idx, ["binarize", "threshold"]])
graph_type = param_df.loc[idx, "graph_type"]
mg = load_metagraph(graph_type, version=BRAIN_VERSION)
mg = preprocess(mg, sym_threshold=True, remove_pdiff=True, **preprocess_params)
left_mb_indicator = mg.meta[class_type].isin(classes) & (
mg.meta["Hemisphere"] == "L"
)
right_mb_indicator = mg.meta[class_type].isin(classes) & (
mg.meta["Hemisphere"] == "R"
)
labels = np.zeros(len(mg.meta))
labels[left_mb_indicator.values] = 1
labels[right_mb_indicator.values] = 2
pred_labels = best_block_df[idx]
pred_labels = pred_labels[pred_labels.index.isin(mg.meta.index)]
assert np.array_equal(pred_labels.index, mg.meta.index), print(idx)
if remove_non_mb: # only consider ARI for clusters with some MB mass
uni_pred = np.unique(pred_labels)
keep_mask = np.ones(len(labels), dtype=bool)
for p in uni_pred:
if np.sum(labels[pred_labels == p]) == 0:
keep_mask[pred_labels == p] = False
labels = labels[keep_mask]
pred_labels = pred_labels[keep_mask]
ari = adjusted_rand_score(labels, pred_labels)
return ari
def compute_ari(idx):
preprocess_params = dict(best_param_df.loc[idx, ["binarize", "threshold"]])
graph_type = best_param_df.loc[idx, "graph_type"]
mg = load_metagraph(graph_type, version=BRAIN_VERSION)
mg = preprocess(mg,
sym_threshold=True,
remove_pdiff=True,
**preprocess_params)
left_mb_indicator = mg.meta["Class 1"].isin(mb_classes) & (
mg.meta["Hemisphere"] == "L")
right_mb_indicator = mg.meta["Class 1"].isin(mb_classes) & (
mg.meta["Hemisphere"] == "R")
labels = np.zeros(len(mg.meta))
labels[left_mb_indicator.values] = 1
labels[right_mb_indicator.values] = 2
pred_labels = best_block_df[idx]
pred_labels = pred_labels[pred_labels.index.isin(mg.meta.index)]
assert np.array_equal(pred_labels.index, mg.meta.index)
ari = adjusted_rand_score(labels, pred_labels)
return ari
def run_experiment(
graph_type=None,
threshold=None,
binarize=None,
seed=None,
param_key=None,
objective_function=None,
implementation="leidenalg",
**kws,
):
np.random.seed(seed)
# load and preprocess the data
mg = load_metagraph(graph_type, version=BRAIN_VERSION)
mg = preprocess(
mg,
threshold=threshold,
sym_threshold=True,
remove_pdiff=True,
binarize=binarize,
)
if implementation == "leidenalg":
if objective_function == "CPM":
partition_type = la.CPMVertexPartition
elif objective_function == "modularity":
partition_type = la.ModularityVertexPartition
partition, modularity = run_leiden(
mg,
temp_loc=seed,
implementation=implementation,
partition_type=partition_type,
**kws,
)
elif implementation == "igraph":
partition, modularity = run_leiden(
mg, temp_loc=seed, implementation=implementation, **kws
)
partition.name = param_key
return partition, modularity
return last
# %% [markdown]
# ## Load data
# In this case we are working with `G`, the directed graph formed by summing the edge
# weights of the 4 different graph types. Preprocessing here includes removing
# partially differentiated cells, and cutting out the lowest 5th percentile of nodes in
# terms of their number of incident synapses. 5th percentile ~= 12 synapses. After this,
# the largest connected component is used.
mg = load_metagraph("G", version="2020-04-01")
mg = preprocess(
mg,
threshold=0,
sym_threshold=False,
remove_pdiff=True,
binarize=False,
weight="weight",
)
meta = mg.meta
# plot where we are cutting out nodes based on degree
degrees = mg.calculate_degrees()
fig, ax = plt.subplots(1, 1, figsize=(5, 2.5))
sns.distplot(np.log10(degrees["Total edgesum"]), ax=ax)
q = np.quantile(degrees["Total edgesum"], 0.05)
ax.axvline(np.log10(q), linestyle="--", color="r")
ax.set_xlabel("log10(total synapses)")
# remove low degree neurons
idx = meta[degrees["Total edgesum"] > q].index
def stashcsv(df, name, **kws):
savecsv(df, name, foldername=FNAME, save_on=True, **kws)
VERSION = "2020-01-29"
print(f"Using version {VERSION}")
graph_type = "Gad"
threshold = 1
weight = "weight"
mg = load_metagraph("Gad", VERSION)
mg = preprocess(
mg,
threshold=threshold,
sym_threshold=True,
remove_pdiff=False,
binarize=False,
weight=weight,
)
print(f"Preprocessed graph {graph_type} with threshold={threshold}, weight={weight}")
out_classes = ["O_dVNC"]
sens_classes = ["sens"]
cutoff = 8
print(f"Finding paths from {sens_classes} to {out_classes} of max length {cutoff}")
adj = nx.to_numpy_array(mg.g, weight=weight, nodelist=mg.meta.index.values)
prob_mat = adj.copy()
row_sums = prob_mat.sum(axis=1)
row_sums[row_sums == 0] = 1
)
def stashobj(obj, name, **kws):
saveobj(obj, name, foldername=FNAME, save_on=SAVEOBJS, **kws)
graph_type = "G"
threshold = 3
binarize = True
# load and preprocess the data
mg = load_metagraph(graph_type, version=BRAIN_VERSION)
mg = preprocess(mg,
threshold=threshold,
sym_threshold=True,
remove_pdiff=True,
binarize=binarize)
#%%
import leidenalg as la
import igraph as ig
def _process_metagraph(mg, temp_loc):
adj = mg.adj
adj = symmetrize(adj, method="avg")
mg = MetaGraph(adj, mg.meta)
nx.write_graphml(mg.g, temp_loc)
param_df.loc[rank_df.index, "rank_AL-roARI"] = rank_df["AL-roARI"]
param_df.loc[rank_df.index, "rank_pairedness"] = rank_df["pairedness"]
param_df.loc[rank_df.index, "rank_adj_pairedness"] = rank_df["adj_pairedness"]
#%%
param_df.sort_values("pairedness", ascending=False)
# %% [markdown]
# # Plot a candidate
# idx = sort_index[2]
idx = "LorenBerglund"
preprocess_params = dict(param_df.loc[idx, ["binarize", "threshold"]])
graph_type = param_df.loc[idx, "graph_type"]
mg = load_metagraph(graph_type, version=BRAIN_VERSION)
mg = preprocess(mg, sym_threshold=True, remove_pdiff=True, **preprocess_params)
labels = np.zeros(len(mg.meta))
pred_labels = best_block_df[idx]
pred_labels = pred_labels[pred_labels.index.isin(mg.meta.index)]
partition = pred_labels.astype(int)
title = idx
class_labels = mg["Merge Class"]
lineage_labels = mg["lineage"]
basename = idx
def augment_classes(class_labels, lineage_labels, fill_unk=True):
if fill_unk:
classlin_labels = class_labels.copy()
def run_experiment(graph_type=None,
threshold=None,
res=None,
binarize=None,
seed=None,
param_key=None):
# common names
if BLIND:
basename = f"{param_key}-"
title = param_key
else:
basename = f"louvain-res{res}-t{threshold}-{graph_type}-"
title = f"Louvain, {graph_type}, res = {res}, threshold = {threshold}"
np.random.seed(seed)
# load and preprocess the data
mg = load_metagraph(graph_type, version=BRAIN_VERSION)
mg = preprocess(
mg,
threshold=threshold,
sym_threshold=True,
remove_pdiff=True,
binarize=binarize,
)
g_sym = nx.to_undirected(mg.g)
skeleton_labels = np.array(list(g_sym.nodes()))
partition, modularity = run_louvain(g_sym, res, skeleton_labels)
partition_series = pd.Series(partition, index=skeleton_labels)
partition_series.name = param_key
if SAVEFIGS:
# get out some metadata
class_label_dict = nx.get_node_attributes(g_sym, "Merge Class")
class_labels = np.array(itemgetter(*skeleton_labels)(class_label_dict))
lineage_label_dict = nx.get_node_attributes(g_sym, "lineage")
lineage_labels = np.array(
itemgetter(*skeleton_labels)(lineage_label_dict))
lineage_labels = np.vectorize(lambda x: "~" + x)(lineage_labels)
classlin_labels, color_dict, hatch_dict = augment_classes(
class_labels, lineage_labels)
# TODO then sort all of them by proportion of sensory/motor
# barplot by merge class and lineage
_, _, order = barplot_text(
partition,
classlin_labels,
color_dict=color_dict,
plot_proportions=False,
norm_bar_width=True,
figsize=(24, 18),
title=title,
hatch_dict=hatch_dict,
return_order=True,
)
stashfig(basename + "barplot-mergeclasslin-props")
category_order = np.unique(partition)[order]
fig, axs = barplot_text(
partition,
class_labels,
color_dict=color_dict,
plot_proportions=False,
norm_bar_width=True,
figsize=(24, 18),
title=title,
hatch_dict=None,
category_order=category_order,
)
stashfig(basename + "barplot-mergeclass-props")
fig, axs = barplot_text(
partition,
class_labels,
color_dict=color_dict,
plot_proportions=False,
norm_bar_width=False,
figsize=(24, 18),
title=title,
hatch_dict=None,
category_order=category_order,
)
stashfig(basename + "barplot-mergeclass-counts")
# TODO add gridmap
counts = False
weights = False
prob_df = get_blockmodel_df(mg.adj,
partition,
return_counts=counts,
use_weights=weights)
prob_df = prob_df.reindex(category_order, axis=0)
prob_df = prob_df.reindex(category_order, axis=1)
probplot(100 * prob_df,
fmt="2.0f",
figsize=(20, 20),
title=title,
font_scale=0.7)
stashfig(basename + f"probplot-counts{counts}-weights{weights}")
return partition_series, modularity
full_meta[f"{sc}_{co}_order"] = full_meta[sc].map(class_value)
total_sort_by.append(f"{sc}_{co}_order")
total_sort_by.append(sc)
full_mg = full_mg.sort_values(total_sort_by, ascending=False)
full_meta = full_mg.meta
n_leaf = full_meta[f"lvl{lowest_level}_labels"].nunique()
n_pairs = len(full_meta) // 2
# %% [markdown]
# ## Random walk stuff
ad_mg = load_metagraph("Gad")
ad_mg = preprocess(ad_mg,
sym_threshold=False,
remove_pdiff=True,
binarize=False)
ad_mg.meta["inds"] = range(len(ad_mg))
ad_adj = ad_mg.adj
meta = ad_mg.meta
source_groups = [
("sens-ORN", ),
("sens-MN", ),
("sens-photoRh5", "sens-photoRh6"),
("sens-thermo", ),
("sens-vtd", ),
("sens-AN", ),
("dVNC", "dVNC;CN", "dVNC;RG", "dSEZ;dVNC"),
("dSEZ", "dSEZ;CN", "dSEZ;LHN", "dSEZ;dVNC"),
("motor-PaN", "motor-MN", "motor-VAN", "motor-AN"),
