Commit 9733bc03 authored by flothoni's avatar flothoni

doc; give more information on way to create clones and compute distributions

Link to #4020
parent 5bf132c9
......@@ -103,6 +103,27 @@ Each clone that has values on the current axes will be displayed in the 'scatter
Each clone that has a sequence will be displayed in the bottom 'segmenter' panel.
### Clone creation
Clone use [boolean mask](https://en.wikipedia.org/wiki/Mask_(computing)) in order to specify attributes.
By default, 3 types of clone is created: constant, distribution and other.
Here are the command and attributes of each common type:
Constant clone correspond to real clone describe into the vidjil file, individually. They are limited to the top clones of a sample.
```javascript
new Clone(data, model, index, C_SIZE_CONSTANT | C_CLUSTERIZABLE | C_INTERACTABLE | C_IN_SCATTERPLOT);
```
Other, or smaller clones, corresponding to the sum of each clones of a given locus, with size dynamicly computed to take into account the current filter and viewable constant clones.
```javascript
new Clone(other, self, index, C_SIZE_OTHER);
```
Distributions clones corresponding to the values given into the distributions data of the vidjil file. They are generated by a function of the model (`loadAllDistribClones`) that automatically agregate data of distributions for each samples. They agregate information on each clones that cannon't be view or show in the interface. They are particularry usefull to simmulate a genescan view in the interface for example.
```javascript
new Clone(data, model, index, C_SIZE_DISTRIB | C_INTERACTABLE | C_IN_SCATTERPLOT );
```
## Integrating the client
......
......@@ -385,6 +385,17 @@ Distributions can be on several axes, like both V/J (here seg3/seg5).
}
```
Distributions are easily computed by the tool `fuse.py` of vidjil. You need to specify a list of distributions waited in the command line. For the example show, the command is:
```bash
python fuse.py -d lenSeqAverage -d seg3,seg5 sample_42.vidjil
```
To get the list of available axis, run `fuse.py` with option `-l`:
```bash
python fuse.py -l
```
Some axis should be added after release. If you want to be able to had new one, you need to modify the function `get_values` in the `fuse.py` script. The new axis should also be added in the client to be taken into account (XXX see axis.js doc XXX).
## `germlines` list \[optional\]\[work in progress, to be documented\]
......
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