Commit 545d2875 authored by Tiago Peixoto's avatar Tiago Peixoto
Browse files

celegans_2019: include new 'corrected' networks

parent 44d8e30a
......@@ -30,9 +30,11 @@ The 'connectivity' edge property corresponds to the total number of EM serial se
To provide complete coverage of the entire nervous system, the data are assembled from multiple animals and include connections added by extrapolation in gaps where no data were available.
For 'synapse' data the edge property 'synapses' contain the number of synapses scored between each pair of cells. These networks differ from the others in not taking into account the sizes of synapses and in showing only connections scored on electron micrographs. It does not include any connections inserted by extrapolation. Thus there are cells showing no connection here that are connected in the the other matrices. Also note, there are more edges in these networks than the total number of synapses scored (synapse lists, Supplementary Information 3). This is because polyads are listed here more than once (once for each postsynaptic cell).
The '_corrected' networks correspond to corrected versions of the network made available in July 2020.
"""
tags = ['Biological', 'Connectome', 'Weighted']
url = 'http://wormwiring.org/series/'
url = 'https://wormwiring.org/pages/adjacency.html'
citation = [('Cook et al., "Whole-animal connectomes of both Caenorhabditis elegans sexes." Nature 571, 63-71 (2019)', 'https://www.nature.com/articles/s41586-019-1352-7')]
icon_hash = '5d1cfbf5f7b45cae742fd520'
ustream_license = None
......@@ -44,7 +46,11 @@ files = [('SI%205%20Connectome%20adjacency%20matrices.xlsx', 'male_chemical', No
('SI%202%20Synapse%20adjacency%20matrices.xlsx', 'male_chemical_synapse', None),
('SI%202%20Synapse%20adjacency%20matrices.xlsx', 'male_gap_junction_synapse', None),
('SI%202%20Synapse%20adjacency%20matrices.xlsx', 'hermaphrodite_chemical_synapse', None),
('SI%202%20Synapse%20adjacency%20matrices.xlsx', 'hermaphrodite_gap_junction_synapse', None)]
('SI%202%20Synapse%20adjacency%20matrices.xlsx', 'hermaphrodite_gap_junction_synapse', None),
('SI%205%20Connectome%20adjacency%20matrices,%20corrected%20July%202020.xlsx', 'male_chemical_corrected', None),
('SI%205%20Connectome%20adjacency%20matrices,%20corrected%20July%202020.xlsx', 'male_gap_junction_corrected', None),
('SI%205%20Connectome%20adjacency%20matrices,%20corrected%20July%202020.xlsx', 'hermaphrodite_chemical_corrected', None),
('SI%205%20Connectome%20adjacency%20matrices,%20corrected%20July%202020.xlsx', 'hermaphrodite_gap_junction_corrected', None)]
def fetch_upstream(force=False):
return fetch_upstream_files(__name__.split(".")[-1], upstream_prefix, files,
......@@ -61,17 +67,20 @@ def parse(alts=None):
continue
with open_upstream_file(name, fname, "rb") as f:
wb = load_workbook(f, read_only=True)
if alt == "male_chemical":
if alt in ["male_chemical", "male_chemical_corrected"]:
g = parse_connectome(wb["male chemical"])
elif alt == "hermaphrodite_chemical":
elif alt in ["hermaphrodite_chemical", "hermaphrodite_chemical_corrected"]:
g = parse_connectome(wb["hermaphrodite chemical"])
elif alt == "male_gap_junction":
elif alt in ["male_gap_junction", "male_gap_junction_corrected"]:
g = parse_connectome(wb["male gap jn asymmetric"])
g.set_directed(False)
elif alt == "hermaphrodite_gap_junction":
g = parse_connectome(wb["herm gap jn asymmetric"])
g.set_directed(False)
elif alt == "male_chemical_synapse":
elif alt == "hermaphrodite_gap_junction_corrected":
g = parse_connectome(wb["hermaphrodite gap jn asymmetric"])
g.set_directed(False)
elif alt in ["male_chemical_synapse"]:
g = parse_connectome(wb["male chem synapse adjacency"], moff=0)
del g.vp["node_type"]
del g.vp["node_subtype"]
......
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