Commit 36577c35 authored by Thonier Florian's avatar Thonier Florian Committed by Mathieu Giraud
Browse files

Doc, add pictures to documentation (user default page)

parent f8cb3f84
......@@ -124,6 +124,12 @@ to learn the essential features of Vidjil.
By hovering the mouse, one also sees the *total*
number of reads for that sample.
<figure> <p style="text-align:center">
<img src="..//pictures/panel_info.png"/>
<p style="text-align:center">Informations panel. Give various informations on patients/runs/sets and on each samples</p>
</p>
</figure>
## The list of clones (left panel)
When they were processed by **vidjil-algo**, clones are described with identifiers
......@@ -159,6 +165,12 @@ then followed by the J gene `TRGJ1*02`, with `6` nucleotides deleted at its star
- A clone with a minus symbol `−` has not been detected in that sample,
but has been detected in another sample that is not currently displayed.
<figure> <p style="text-align:center">
<img src="..//pictures/panel_list.png"/>
<p style="text-align:center">The list of clones. Some clonotype here are merged together, some tagged. Other show warning icon.</p>
</p>
</figure>
### Detailed information on each clone
The “🛈” button opens a window showing detailed information (V(D)J designation,
e-value, number of reads) about each clone.
......@@ -206,7 +218,11 @@ It shows the most frequent clones of each sample, tracked into every sample.
- If your dataset contains sampling dates (for example for diagnosis/follow-up samples), you can switch between sample keys and dates in “settings \> sample key”
<figure> <p style="text-align:center">
<img src="..//pictures/panel_graph.png"/>
<p style="text-align:center">Timeline graphic that allow to follow clonotype size variation during time.</p>
</p>
</figure>
## The plot view and the plot presets
......@@ -223,7 +239,12 @@ When there is only one sample, two such views are shown.
- On the bar plots, the Y axis corresponds to the order of clones inside each bar.
See [axis page](axis.md) to get more informations on available axis and avalability of them inside client components.
<figure> <p style="text-align:center">
<img src="..//pictures/panel_scatterplot.png"/>
<p style="text-align:center">Default scatterplot at analysis loading (axis V/J). See [axis page](axis.md) to get more informations on available axis and avalability of them inside client components.</p>
</p>
</figure>
## Status bar
......@@ -247,6 +268,12 @@ The sequence panel shows, for the selected clones:
- some *features* on these sequences
<figure> <p style="text-align:center">
<img src="..//pictures/panel_sequence.png"/>
<p style="text-align:center">For each clonotype, name and sequences are shown. Some other feature can also be added.</p>
</p>
</figure>
### Selecting clones for inspection
Clones can be (un)selected by several ways:
......@@ -263,6 +290,12 @@ The `cluster` button will create a cluster with the selected clones
Such a cluster will appear as a single clone,
with the first (largest) selected clone acting as its representative.
<figure> <p style="text-align:center">
<img src="..//pictures/panel_list_merge_2.png"/>
<p style="text-align:center">Even after a merge, it still possible to access to all information of subclonotype, and if needed to remove them from the merge.</p>
</p>
</figure>
### Align
The `align` button aligns all the selected sequences,
......@@ -307,6 +340,7 @@ These buttons will send the sequences of selected clones to them for analysis an
Assignment to the [19 known major subsets](https://www.ncbi.nlm.nih.gov/pubmed/22415752)
of stereotyped antigen receptor sequences for CLL
### Sequence Features
Depending on the analysis software and on its configuration, there can be positions of genes or specific regions of interest that can be highlighted.
......@@ -342,6 +376,13 @@ you can process your data and save the results of your analysis.
## Patients
<figure> <p style="text-align:center">
<img src="..//pictures/table_db_content_patient_list.png"/>
<p style="text-align:center">An example of database content and organization.</p>
</p>
</figure>
<i>
⚠️ The public <http://app.vidjil.org/> server is for Research Use Only
and is not compliant for clinical use.
......@@ -417,6 +458,13 @@ which is not the case for the results (unless the user wants so).
You can see which samples have been processed with the selected
process, and access to the results (`See results`, bottom right).
<figure> <p style="text-align:center">
<img src="..//pictures/table_db_content_patient_0_multi_config.png"/>
<p style="text-align:center">Example of demo patient LIL-L3. This patient is available from demo account. Their are 5 samples analyzed with default configuration.</p>
</p>
</figure>
### Adding a sample
To add a sample (`+ add samples`), you must add at least one sample file. Each sample file must
......
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