Commit d47b12f7 authored by Marc Duez's avatar Marc Duez
parents df4447a1 20b2aac2
......@@ -801,6 +801,7 @@ span.logo {
width: 475px;
}
.menu-highlight {
display: none;
position: relative;
float: left;
width: 250px;
......
......@@ -801,6 +801,7 @@ span.logo {
width: 475px;
}
.menu-highlight {
display: none;
position: relative;
float: left;
width: 250px;
......
......@@ -946,6 +946,7 @@ span.logo
}
.menu-highlight {
display: none;
position: relative;
float: left;
width: @width_highlight;
......
......@@ -911,7 +911,12 @@ Sequence.prototype = {
h.css = "highlight_seq"
var j = 0
for (var k=h.start; j<raw_seq.length; k++) { // End condition on j, not on k
if (this.seq[k] != '-') h.seq += raw_seq[j++] ; else h.seq += "&nbsp;"
var c = "&nbsp";
if (this.seq[k] != '-') {
var cc = raw_seq[j++]
if ((cc != '_') && (cc != ' ')) c = cc ;
}
h.seq += c
}
}
......
......@@ -92,6 +92,14 @@ Shortcut.prototype = {
if(e.shiftKey || e.metakey) db.reload()
break;
default:
if ((key >= 96) && (key <= 105)) { // Numeric keypad, 0-9
var select_preset = document.getElementById("select_preset")
select_preset.selectedIndex = key - 95
try {
sp.changePreset(select_preset)
}
catch (err) { } // There can be an error if the preset does not exist
}
}
}
......
......@@ -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
......@@ -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.
......@@ -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”
......@@ -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+ | Change the selected germline/locus |
| =d=: TRD, TRD+ | change the selected germline/locus |
| =h=: IGH, IGH+ | |
| =l=: IGL | |
| =k=: IGK, IGK+ | |
......
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