get_connected_skeletons behaves unexpectedly

[schlegelp]

Seba encountered this: get_connected_skeletons appears to return incomplete list of partners.

Minimal example:

> av1a1Neurons = read.neurons.catmaid(c(2659704, 2684792))
> cn = get_connected_skeletons(av1a1Neurons, min_synapses = 10)
> names(cn)
[1] "2101395"  "4947032"  "6180224"  "6189928"  "6199308"  "6199551"  "11545803"

cn should contain order 50 neurons given a 10 synapse threshold.

[jefferis]

What happens if you retry using the skids rather than neuronlist?

…

Sent from my iPhone

On 29 May 2019, at 10:10, Philipp Schlegel ***@***.***> wrote: Seba encountered this: get_connected_skeletons appears to return incomplete list of partners. Minimal example: > av1a1Neurons = read.neurons.catmaid(c(2659704, 2684792)) > cn = get_connected_skeletons(av1a1Neurons, min_synapses = 10) > names(cn) [1] "2101395" "4947032" "6180224" "6189928" "6199308" "6199551" "11545803" cn should contain order 50 neurons given a 10 synapse threshold. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[schlegelp]

get_connected_skeletons accepts only neuron lists

[jefferis]

Sorry, I hadn't noticed that this was a catnat function. I guess that's one for you @alexanderbates. But in general, I would use the catmaid functions listed at https://jefferis.github.io/rcatmaid/reference/index.html#section-synaptic-connections. In this case https://jefferis.github.io/rcatmaid/reference/catmaid_get_connector_table.html is the closest match.

[jefferis]

Sorry https://jefferis.github.io/rcatmaid/reference/catmaid_query_connected.html

> catmaid_query_connected(c(2659704, 2684792), minimum_synapses = 10)
$outgoing
       skid partner syn.count num_nodes
127 2659704 6199551        18     10114
14  2659704 6199308        15      2867
62  2659704 6180224        14     10358
318 2684792 4947032        10      6584
741 2659704 6189928        10      3943

$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
71  2659704    40749        36      7629
63  2684792    22976        33     13867
34  2659704    57192        32      3476
64  2659704  3780040        30      9383
58  2659704    55125        29      4815
20  2659704  3983385        28      6582
60  2659704    52106        28      4270
54  2659704    51080        27      6772
95  2684792    39668        26      9239
32  2659704    57003        25      5823
87  2684792    21999        25     10794
24  2659704 11545803        23     35685
88  2659704  2101395        23     16633
26  2659704    65762        20      6527
45  2659704    57246        20      5104
94  2659704    39668        20      9239
82  2659704    73937        19      5289
97  2659704    23597        18     10474
163 2659704    57499        16      6664
2   2684792  2846667        15      8525
18  2659704  1710793        15      9464
76  2659704  4187651        15      4738
53  2684792 11519897        14     23937
86  2659704    21999        14     10794
57  2684792   775731        13      4794
72  2684792    40749        13      7629
79  2684792  2766186        13     21321
164 2684792    57499        13      6664
16  2659704    37250        12      9813
41  2659704   531931        12      6265
52  2659704 11519897        12     23937
56  2659704   775731        12      4794
180 2684792    35246        12      4851
21  2684792  3983385        11      6582
101 2659704    24622        11      4433
102 2684792    24622        11      4433
120 2659704    22132        11      8517
143 2659704    57307        11      5296
179 2659704    35246        11      4851
25  2684792 11545803        10     35685
65  2684792  3780040        10      9383
123 2659704    68697        10      4968