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75 changes: 24 additions & 51 deletions docs/data_analysis.md
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Expand Up @@ -16,43 +16,43 @@ The second step is the choice of the level to which clonal complexes will be for

A goeBURST _Output_ tab will appear and display the goeBURST algorithm results. It will contain information about the Clonal Complexes (CCs), namely the Sequence Types that compose them and what edges (the links between STs) were drawn in each CC.

![output](https://github.com/phyloviz/phyloviz-main/blob/master/docs/_images/GEB2.png)
![output](_images/GEB2.png)

In order to display the goEburst tree view, it is necessary to expand the typing data on the DataSets' tab, if it os not already expanded.
In order to display the goEburst tree view, it is necessary to expand the typing data on the DataSets' tab, if it is not already expanded.

![display](https://github.com/phyloviz/phyloviz-main/blob/master/docs/_images/GEB3.png)
![display](_images/GEB3.png)

Double clicking on the goeBURST item that is now on the Dataset tree menu will show the display. The clonal complexes will be arbitrarily numbered starting from 0 (for the CC with most STs) and contains all the data relevant to the goeBURST analysis (STs in each group and the drawn SLVs edges). The following screenshot summarizes the output for a single clonal complex with the test dataset used.

![largest cc](http://www.phyloviz.net/wiki/dataanalysis/goeBURSTcc0display.png)

Multiple groups can be displayed simultaneously by selecting them, using the CTRL /CMD and/or SHIFT keys.

![multiple groups](https://github.com/phyloviz/phyloviz-main/blob/master/docs/_images/GEB4.png)
![multiple groups](_images/GEB4.png)

## goeBURST Full MST algorithm

Using an extension of the goeBURST rules up to \\(n\\)LV level (where \\(n\\) equals to the number of loci your dataset uses), a Minimum Spanning Tree-like structure can be drawn. Select _goeBURST Full MST_ in the _Compute_ options to draw it. Contrary to the standard goeBURST, the link statistics are not presented. After computation, double click on the _goeBURST Full MST_ that appears under the dataset heading to visualize the result.

![mst result](https://github.com/phyloviz/phyloviz-main/blob/master/docs/_images/GEB5.png)
![mst result](_images/GEB5.png)

New options appear on the display: The _Level_ selector and two new buttons _Get Groups_ and _Save Groups_. The _Level_ represents the _Locus Variant_ level and allows the removal of all the links greater than the number represented. The user can use the up and down arrows or directly edit the number by clicking on it. The _Get Groups_ button allows separate the display of groups that are not connected at the level chosen in order to simplify the analysis of larger datasets. This will generate a display very similar to that of goeBURST, but at a higher link level. The Save Groups creates an extra column in the isolate data with the title label _goeBURST MST[\\(x\\)]_ with \\(x\\) being equal to the level used to create the groups.

Decreasing the _Level_ selector, allows the user to see how clonal complexes would relate to each other at a certain level. Level 1, 2 and 3 are equivalent to calculating goeBURST at those levels (SLV,DLV and TLV respectively). The following images shows what happens to the dataset when you decrease the level. Level 4 is not displayed since no new groups are formed at that level.

![new groups](https://github.com/phyloviz/phyloviz-main/blob/master/docs/_images/GEB6.png)
![new groups](_images/GEB6.png)

At level 5 only two groups are formed in the sample dataset.

![more grouping](https://github.com/phyloviz/phyloviz-main/blob/master/docs/_images/GEB7.png)
![more grouping](_images/GEB7.png)

At level 3 (TLV level) some singletons appear. Level 4 is not shown since no changes were observed in the graph. This means that there are no two STs in the dataset that differ in 4 of the loci of their profiles.

![another example](https://github.com/phyloviz/phyloviz-main/blob/master/docs/_images/GEB8.png)
![another example](_images/GEB8.png)

At level 2 , 6 groups appear with 4 or more STs each.

![one more](https://github.com/phyloviz/phyloviz-main/blob/master/docs/_images/GEB9.png)
![one more](_images/GEB9.png)

And finally at level 1, the equivalent of the most commonly used Clonal Complex definition by goeBURST, 17 groups with 2 or more STs are formed and there are 25 singletons on the dataset.

Expand All @@ -61,68 +61,41 @@ And finally at level 1, the equivalent of the most commonly used Clonal Complex
Selecting the Hierarchical Clustering opens the dialog where you can select what method you want to apply.
The first step is choosing the _Distance_ to be used. Currently the hamming distance is the only one available, but others could be implemented.

![distance](https://github.com/phyloviz/phyloviz-main/blob/master/docs/_images/HC1.png)
![distance](_images/HC1.png)

The second step is to select the _Method_. You can choose between complete-linkage, single-linkage, UPGMA (Unweighted Pair Group Method with Arithmetic mean) and WPGMA (Weighted Pair Group Method with Arithmetic mean). Selecting the method corresponds to selecting the criterion of minimal dissimilarity.

![method](https://github.com/phyloviz/phyloviz-main/blob/master/docs/_images/HC2.png)
![method](_images/HC2.png)

A Hierarchical Clustering _Output Tab_ will appear and display the results of the application of the chosen method. A _Leaf_ represents a Sequence Type and a _Union_ represents a group that results of joining Leafs or Unions with Leafs.
This process of joining is displayed step by step by the algorithm in the _Output's Tab_.
Finally we have the number of ties occured. The tie break applied is to always choose the first one found.

![output](https://github.com/phyloviz/phyloviz-main/blob/master/docs/_images/HC3.png)
![output](_images/HC3.png)

In order to display the dendogram view, it is necessary to expand the typing data on the Datasets' tab, if it is not already expanded.

![expanding](https://github.com/phyloviz/phyloviz-main/blob/master/docs/_images/HC4.png)
![expanding](_images/HC4.png)

It shoud appear an icon corresponding to the hierarchical clustering computation

![expanded](https://github.com/phyloviz/phyloviz-main/blob/master/docs/_images/HC5.png)
![expanded](_images/HC5.png)

Double clicking on the Hierarchical Clustering item will show the display. This type of clustering is represented in the format of a dendogram.
The following screenshot summarizes the output for the previous dataset. Sometimes it is necessary to fit the image to see all the display at once. To do this, please right click on the mouse over the display.

![display](https://github.com/phyloviz/phyloviz-main/blob/master/docs/_images/HC6.png)
![display](_images/HC6.png)

Some features were added to the visualization to improve and facilitate the analysis.
These features are the following:
1. Height scale

The display can be vertically stretched or shrinked, using the scroll in evidence in the next figure.

![heightscale](https://github.com/phyloviz/phyloviz-main/blob/master/docs/_images/HC7.png)

2. Width scale

The display can be horizontally stretched or shrinked, using the scroll in evidence in the next figure.

![widthscale](https://github.com/phyloviz/phyloviz-main/blob/master/docs/_images/HC8.png)

3. Options Panel

As it can be seen in the next figure, several options can be applied to the display.

![options](https://github.com/phyloviz/phyloviz-main/blob/master/docs/_images/HC11.png)

For instance, the _Info_ option will add an output tab such that each time we click on an ST over the display, it will add to that output tab the information about the profile and about the anciliary data. As an example, in the next figure, the ST 20 was selected.


![info_options](https://github.com/phyloviz/phyloviz-main/blob/master/docs/_images/HC12.png)

The _Distance labels_ option will display the value of the distance between each taxa pair. The other options, _Linear Nodes_ and _Re-scale Edges_ changes the size of ST nodes and edges, respectively. By default, the size of each ST node in the display is logarithmic in the number of the isolates that have that ST. By changing to linear, the size in the display will become linearly proportional. With respect to the edges, the default size is lineary proportional to the original size and thus, applying the _Re-scale Edges_ option, it will because logarithmically.

4. Search ST

Using the text panel that is in evidence in the next figure, it is possible to search for a given ST.

![search](https://github.com/phyloviz/phyloviz-main/blob/master/docs/_images/HC9.png)

5. Filter by distance (cut off threshold)
![filter](https://github.com/phyloviz/phyloviz-main/blob/master/docs/_images/HC10.png)
6. Export image

These features are the following:
1. Height scale
2. Width scale
3. Options Panel
4. Search ST
5. Filter by distance (cut off threshold)
6. Export image

See section <a href="http://phyloviz.readthedocs.io/en/latest/display_and_visualization.html">display and visualization</a> for more information on these features.


## Neighbor Joinning
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32 changes: 24 additions & 8 deletions docs/display_and_visualization.md
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Expand Up @@ -7,14 +7,30 @@ After running the selected algorithm, you will notice that the program then trie
The Display tab offers the user the ability to search for an isolate, Highlight the SLVs and DLVs, control the animation speed, select diferent diferent or multiple groups. You can fit any displayed graphs to the window by right-clicking any open space (i.e. with no link or ST node) on the window.

Click to see how to use the features:
* [basic interface](http://www.phyloviz.net/wiki/displayinterface/BasicInterface.png),
* [SLV/DLV highlighting](http://www.phyloviz.net/wiki/displayinterface/highlighting.png),
* [ST search](http://www.phyloviz.net/wiki/displayinterface/search.png),
* [information area](http://www.phyloviz.net/wiki/displayinterface/InfoArea.png),
* [force control menu](http://www.phyloviz.net/wiki/displayinterface/ControlMenu.png),
* [high level edges](http://www.phyloviz.net/wiki/displayinterface/HighLevelEdges.png),
* [changing group founder](http://www.phyloviz.net/wiki/displayinterface/ChangingGroupFounder.png),
* [saving results](http://www.phyloviz.net/wiki/displayinterface/SavingResults.png).

1. ***Common*** *features*
* [ST search](http://www.phyloviz.net/wiki/displayinterface/search.png),
* [information area](http://www.phyloviz.net/wiki/displayinterface/InfoArea.png),
* *Exporting Image*

2. ***GoEburst*** *and* ***Full GoEburst*** *features*
* [basic interface](http://www.phyloviz.net/wiki/displayinterface/BasicInterface.png),
* [SLV/DLV highlighting](http://www.phyloviz.net/wiki/displayinterface/highlighting.png),
* [high level edges](http://www.phyloviz.net/wiki/displayinterface/HighLevelEdges.png),
* [changing group founder](http://www.phyloviz.net/wiki/displayinterface/ChangingGroupFounder.png),
* [saving results](http://www.phyloviz.net/wiki/displayinterface/SavingResults.png).

3. ***GoEburst***, ***Full GoEburst*** *and* ***Neighbor Joinning*** *features*
* [force control menu](http://www.phyloviz.net/wiki/displayinterface/ControlMenu.png),

4. ***Neighbor Joinning*** *features*
* Changing the tree layout

5. ***Hierarchical Clustering*** *and* ***Neighbor Joinning*** *features*
* [height scale](_images/HC7.png),
* width scale
* filter by distance (cut off threshold)


## Color conventions

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