Commit 087f2727 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

browser.org: update help

parent 094cb794
...@@ -71,12 +71,12 @@ Otherwise, such =.vidjil= files can be obtained: ...@@ -71,12 +71,12 @@ Otherwise, such =.vidjil= files can be obtained:
** The info panel (upper left panel) ** The info panel (upper left panel)
- analysis :: name of the configuration file used for displaying the data - analysis :: name of the configuration file used for displaying the data
- locus :: germline used for analyzing the data. In case of multi-germline - locus :: germline used for analyzing the data. In case of multi-locus
data, you can select what germline should be displayed. data, you can select what locus should be displayed.
- point :: name of the current point (you can change the selected point by clicking on - 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”). 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) - 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. See [[Number of segmented reads]] below.
- total :: total number of reads for that point - total :: total number of reads for that point
...@@ -90,8 +90,7 @@ Otherwise, such =.vidjil= files can be obtained: ...@@ -90,8 +90,7 @@ Otherwise, such =.vidjil= files can be obtained:
- The “i” button displays additional information on each clone. - 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 can be sorted on V genes, J genes or clone abundance.
the list you need to click respectively on “V sort”, “J sort” or “sort”.
The “+” and “-” allow respectively to un-merge or re-merge all clones that have The “+” and “-” allow respectively to un-merge or re-merge all clones that have
already been merged. already been merged.
...@@ -112,13 +111,15 @@ The time graph is hidden with there is only one timepoint. ...@@ -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” - 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. - 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 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” to focus on the clones, then to display them ones according to either their “clone length”
...@@ -297,12 +298,13 @@ There can be several causes leading to bad ratios: ...@@ -297,12 +298,13 @@ There can be several causes leading to bad ratios:
| =←= and =→= | navigate between samples | | =←= and =→= | navigate between samples |
| =Shift-←= and =Shift-→= | decrease or increase the number of displayed clones | | =Shift-←= and =Shift-→= | decrease or increase the number of displayed clones |
| numeric keypad, =0-9= | switch between available preset modes |
| =a=: TRA | | | =a=: TRA | |
| =b=: TRB | | | =b=: TRB | |
| =g=: TRG | | | =g=: TRG | |
| =d=: TRD, TRD+ | Change the selected germline/locus | | =d=: TRD, TRD+ | change the selected germline/locus |
| =h=: IGH, IGH+ | | | =h=: IGH, IGH+ | |
| =l=: IGL | | | =l=: IGL | |
| =k=: IGK, IGK+ | | | =k=: IGK, IGK+ | |
......
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