Commit 7625d764 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/vidjil-format.md: draft documentation on distributions

See #4020.
parent e1b0ee25
......@@ -149,6 +149,7 @@ do a correct gathering.
}
```
## `.analysis` file
This file reflects the annotations a user could have done within the Vidjil web application or some other tool.
......@@ -347,6 +348,44 @@ In the `.analysis` file, this section is intended to describe some specific clon
}
```
## `distributions`: providing statistics on full clonal populations
In some situations, one would like to represent whole distributions of clones
according to "axes" such as V/J distribution or length.
It is possible to specify in the `.vidjil` file such `"distributions"`
without detailing the full list of clones, hence keeping a relatively small file
and enabling fast post-processing or visualizations.
In the example below, 5 clones (totaling 6 reads) have a length of 223.
Distributions can be on several axes, like both V/J (here seg3/seg5).
``` javascript
{
"distributions":
{
"keys": ["clones", "reads"],
"repertoires": {
"sample_42": [
{
"axes": ["lenSeqAverage"],
"values": { "223": [5, 6], "232": [1, 7], "260": [5, 20] }
},
{
"axes": ["seg3", "seg5"],
"values": {
"IGHJ3": {"IGHV4-39": [5, 20]},
"IGHJ4": {"IGHV3-23": [1, 7], "IGHV3-64": [1, 1]},
"IGHJ6": {"IGHV1-24": [2, 3], "IGHV1-8": [2, 2]}
}
}]
}
}
}
}
```
## `germlines` list \[optional\]\[work in progress, to be documented\]
extend the `germline.data` default file with a custom germline
......
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