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natverse / rcatmaid

R package providing API access to the CATMAID web image annotation tool
https://natverse.github.io/rcatmaid
GNU General Public License v3.0
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catmaid_query_connected silently ignores <5 confidence connections #113

Closed schlegelp closed 5 years ago

schlegelp commented 5 years ago

Minimal example:

> cn = catmaid_query_connected(c(2659704, 2684792))
> head(cn$incoming)
      skid partner syn.count num_nodes
1  2659704 2846667        52      8525
4  2659704   23829        52     17668
39 2659704   39254        43     20796
62 2659704   22976        42     13867

syn.count does not match numbers in CATMAID:

2659704 2846667        55      8525
2659704   23829        53     17668
2659704   39254        46     20796
2659704   22976        43     13867

For example, 2659704->2846667 has confidences:

confidence:count
1:0 
2:0 
3:2 
4:1
5:52

Following CATMAID's connectivity table widget, the intuitive solution would be to include all confidences by default and have a optional confidence_threshold parameter.