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vidjil
vidjil
Commits
087f2727
Commit
087f2727
authored
Mar 06, 2015
by
Mathieu Giraud
Browse files
browser.org: update help
parent
094cb794
Changes
1
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087f2727
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@@ -71,12 +71,12 @@ Otherwise, such =.vidjil= files can be obtained:
** The info panel (upper left panel)
- analysis :: name of the configuration file used for displaying the data
- locus :: germline used for analyzing the data. In case of multi-
germline
data, you can select what
germline
should be displayed.
-
point
:: name of the current point (you can change the selected point by clicking on
- locus :: germline used for analyzing the data. In case of multi-
locus
data, you can select what
locus
should be displayed.
-
sample
:: name of the current point (you can change the selected point by clicking on
another point in the graph). The name can be edited (“edit”).
- date :: when the run was performed (edit either with “...”, or with the database, on the patient tab)
- segmented :: number of reads where Vidjil found a CDR3, for that
point.
- segmented :: number of reads where Vidjil found a CDR3, for that
sample
See [[Number of segmented reads]] below.
- total :: total number of reads for that point
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@@ -90,8 +90,7 @@ Otherwise, such =.vidjil= files can be obtained:
- The “i” button displays additional information on each clone.
- The list can be sorted on V genes, J genes or concentrations. At the top of
the list you need to click respectively on “V sort”, “J sort” or “sort”.
- The list can be sorted on V genes, J genes or clone abundance.
The “+” and “-” allow respectively to un-merge or re-merge all clones that have
already been merged.
...
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@@ -112,13 +111,15 @@ The time graph is hidden with there is only one timepoint.
- If your dataset contains sampling dates (for example in a MRD setup), you can switch between point keys and dates in “settings > point key”
** The
grid
view
** The
plot
view
- The axes of the plot (by default “V gene” / “J gene”) can be changed.
- The "plot" menu allow to change the (grid plot, bar plot) as well as the X and Y axes of these plot
Some presets are available.
-
Some presets are available in the “analysis” menu
.
-
In the bar plot mode, the Y axis corresponds to the order of clones inside each bar
.
- The “focus“ button (bottom right) allows to further analyze a selection of clones.
To exit the focus mode, click on the “X” near the search box.
To further analyze a set of clones sharing a same V and J, it is often useful
to focus on the clones, then to display them ones according to either their “clone length”
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@@ -297,12 +298,13 @@ There can be several causes leading to bad ratios:
| =←= and =→= | navigate between samples |
| =Shift-←= and =Shift-→= | decrease or increase the number of displayed clones |
| numeric keypad, =0-9= | switch between available preset modes |
| =a=: TRA | |
| =b=: TRB | |
| =g=: TRG | |
| =d=: TRD, TRD+ |
C
hange the selected germline/locus |
| =d=: TRD, TRD+ |
c
hange the selected germline/locus |
| =h=: IGH, IGH+ | |
| =l=: IGL | |
| =k=: IGK, IGK+ | |
...
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