Commit 8a2360a5 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/user.md: sample graph, reword, more details on the gray zone

parent 53f512af
......@@ -157,25 +157,34 @@ calculated over all the samples in the sample set.
## The sample graph
The sample graph is hidden when there is only one sample. It shows the most frequent clones of each sample, tracked into every sample.
The number of displayed clones can be changed with the filter menu.
The sample graph is displayed as soon as there are at least two samples.
It shows the most frequent clones of each sample, tracked into every sample.
- The current sample is highlighted with a vertical gray bar. You can select another sample by clicking on it or using `←` and `→`.
- The gray areas at the bottom of the graph show, for each sample, the resolution (1 read / 5 reads).
- By default, the graph shows clones present in the top 20 of any sample.
See below "[Can I see all the clones ?](#can-i-see-all-the-clones-and-all-the-reads)".
You can instead choose to show only the clones present in the current sample
with “filter \> focus on clones of one sample“.
- When a clone gathers very few reads, typically less than five,
its concentration ratio is not significant and it is shown by a `+` in the clone list.
Such clones appear in the sample graph in a *gray zone*.
They should be considered as “detected, but not quantifiable“,
and different concentrations in the gray zone should not be compared.
- A menu to show or hide samples either one by one or all of them is present on the graph.
This menu is shown when hovering the "X/Y" button at the top-right of the graph.
The X and Y values correspond to the shown and total number of samples.
In this menu, clicking one time on one sample in the menu focuses on this sample.
Double clicking on one sample switches its state between shown or hidden.
- Samples can be reordered by dragging their label.
- You can reorder the samples by dragging them, and hide some samples by double clicking on their label.
- Samples can be hidden by double-clicking on their label.
At the top-right of the graph, a button such as `5/8`
shows how many samples are displayed (here `5`) and the total number of samples (here `8`).
This button reveals a menu where
any samples can be selected (single click),
or shown or hidden (double click),
as well as options to show or hide all samples.
- 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”
- By default, the graph shows clones present in any sample.
You can instead choose to show only the clones present in the selected sample with “filter \> focus on clones of one sample“.
## The plot view and the plot presets
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