Commit d2113051 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

doc/user.md: screenshot captions, bikeshed and details

parent 84e9895d
......@@ -126,9 +126,14 @@ to learn the essential features of Vidjil.
<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>
<i>
The information panel.
The patient/run/set or sample information may contain tags such as `#T-ALL`.
In this sample,
V(D)J recombinations were detected
in about 82% of the reads.</p>
</i>
## The list of clones (left panel)
......@@ -167,9 +172,19 @@ then followed by the J gene `TRGJ1*02`, with `6` nucleotides deleted at its star
<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>
<i>The list of clones.
The main clonotype is
`IGHV3-9*01 7/CCCGGA/17 IGHJ6*02`,
with 7 deletions on the 3' side of the V,
17 deletions on the 5' side of the J,
and a insertion of `CCCGGA` in the N region.
Here the settings shorten this
name by not showing the `*01` allele.
This clonotype is actually a cluster (+)
of sub-clones.
The `TRGV10 4//8 JP2` clonotype has a warning.
</i>
### Detailed information on each clone
The “🛈” button opens a window showing detailed information (V(D)J designation,
......@@ -220,8 +235,11 @@ It shows the most frequent clones of each sample, tracked into every sample.
<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>
<i>
This sample graph show the evolution of a T-ALL patient relapsing at D+268/D+308 with a clonotype
that was not the main one at the diagnosis.The view was filtered to show only clonotypes of interest.
</i>
</figure>
## The plot view and the plot presets
......@@ -241,10 +259,13 @@ When there is only one sample, two such views are shown.
<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>
</p>
</figure>
<i>
Grid view with the default [axes](axes.md) (V/5' and J/3' gene) focusing on the TRG locus. The TRGV10/TRGJP10 clonotype appears in red because it has been tagged as `clone 1` from the clonotype list. Clicking on IGH focus on the IGH locus.
</i>
## Status bar
......@@ -292,9 +313,9 @@ 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>
<i>The top clonotype is actually a cluster of several sub-clonotypes. It is still possible to access to all the information of such sub-clonotype. Clicking on "x" remove a sub-clonotype from the cluster.</p>
</i>
### Align
......
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