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phyloviz · Jul 13, 2016 · 1b815fe · 1b815fe
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diff --git a/docs/_images/DataSetloaded.png b/docs/_images/DataSetloaded.png
diff --git a/docs/_images/Export.png b/docs/_images/Export.png
diff --git a/docs/_images/IsolateData.png b/docs/_images/IsolateData.png
diff --git a/docs/_images/IsolateDataTable.png b/docs/_images/IsolateDataTable.png
diff --git a/docs/_images/LoadDataSet_1.png b/docs/_images/LoadDataSet_1.png
diff --git a/docs/_images/LoadDataSet_2.png b/docs/_images/LoadDataSet_2.png
diff --git a/docs/_images/LoadDataSet_3.png b/docs/_images/LoadDataSet_3.png
diff --git a/docs/_images/LoadDataset.png b/docs/_images/LoadDataset.png
diff --git a/docs/_images/RegexExample.png b/docs/_images/RegexExample.png
diff --git a/docs/_images/TreeViewDisplay.png b/docs/_images/TreeViewDisplay.png
diff --git a/docs/_images/TreeViewSelections.png b/docs/_images/TreeViewSelections.png
diff --git a/docs/_images/TypingData.png b/docs/_images/TypingData.png
diff --git a/docs/_images/TypingDataTable.png b/docs/_images/TypingDataTable.png
diff --git a/docs/_images/goeBURST1.png b/docs/_images/goeBURST1.png
diff --git a/docs/_images/goeBURST2.png b/docs/_images/goeBURST2.png
diff --git a/docs/_images/goeBURSTcc0display.png b/docs/_images/goeBURSTcc0display.png
diff --git a/docs/_images/samplefiles.png b/docs/_images/samplefiles.png
diff --git a/docs/_images/treeView.png b/docs/_images/treeView.png
diff --git a/docs/data_analysis.md b/docs/data_analysis.md
@@ -8,11 +8,11 @@ In the current version of PHYLOViZ, you can analyze your data using the goeBURST
 
 Selecting the goeBURST algorithms opens the dialog for the goeBURST algorithm. The algorithm was originally described in the article [Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach](http://www.biomedcentral.com/1471-2105/10/152). The first step is choosing the _Distance_ to be used. Currently eBURST Distance is the only one available, but others could be implemented. The eBURST distances follows the tiebreak rules discussed in the article. 
 
-![distance](http://www.phyloviz.net/wiki/dataanalysis/goeBURST1.png)
+![distance](_images/goeBURST1.png)
 
 The second step is the choice of the level to which clonal complexes will be formed. The usual default for MLST analysis is SLV Level. Choosing DLV or TLV level will take longer calculation times, but could provide some insight to the relationships between clonal complexes formed at SLV and DLV level respectively.
 
-![level](http://www.phyloviz.net/wiki/dataanalysis/goeBURST2.png)
+![level](_images/goeBURST2.png)
 
 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.
 
@@ -24,7 +24,7 @@ In order to display the goEburst tree view, it is necessary to expand the typing
 
 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)
+![largest cc](_images/goeBURSTcc0display.png)
 
 Multiple groups can be displayed simultaneously by selecting them, using the CTRL /CMD and/or SHIFT keys.
 
@@ -103,19 +103,19 @@ See section <a href="http://phyloviz.readthedocs.io/en/latest/display_and_visual
 Selecting the Neighbor Joinning algorithm opens the dialog where you can select what method you want to apply.
 The first step is choosing the _Distance_ to be used.
 
-![distance](./images/)
+![distance](_images/NJ1.png)
 
 The second step is to select the _Criteria_. You can choose between Saitou-Nei and Studier-Keppler criterion.
 
-![method](./images/)
+![method](_images/NJ2.png)
 
 A Neighbor Joinning _Output Tab_ will appear and display the results of the application of the chosen method. The information displayed represents the same as the Hierarchical Clustering _Output Tab_.
 
-![output](./images/)
+![output](_images/NJ3.png)
 
 Double clicking on the Neighbor Joinning item will show the display. By default it is represented in the format of a radial tree. The following screenshot summarizes the output for the previous dataset.
 
-![display](./images/)
+![display](_images/NJ4.png)
 
 Some features were added to the visualization to improve and facilitate the analysis. 
 These features are the following:
@@ -124,4 +124,5 @@ These features are the following:
 3. Filter by distance
 4. Export image
 
-![display features](./images/)
+![display features](_images/NJ5.png)
+
diff --git a/docs/loading_data.md b/docs/loading_data.md
@@ -4,49 +4,49 @@
 
 To be able to analize and visualize your data, PHYLOViZ needs two separate files: One file contains the allelic profile data of the method you are using (Typing Data), while the other will contain accessory data (Isolate Data).
 
-![sample files](http://www.phyloviz.net/wiki/dataloading/samplefiles.png)
+![sample files](_images/samplefiles.png)
 
 The Typing data should be a tab separated file containing the allelic profiles, formatted as follows: the first line should contain the column headers (usually markers or MLST locus identifiers). The first column should be the allelic profile identifier (Sequence Type number). The following columns are the loci used in the analysis.
 
 If the Isolate data file is not used, the Typing data file should also represent the number of repeated profiles in a collection, that is to say that if a given profile appears in a collection n times it should be repeated in the Typing data file n times. In case of an Isolate data file is used the frequency of each type will be represented by the number of entries with a given Sequence type, in the Isolate file only and the frequency represented by repeated profiles in the Typing data file will not be used
 
-You can find an example of MLST data correctly formatted [here](http://www.phyloviz.net/wiki/dataloading/sampleAPfile.txt). Note that in this file several STs are represented by more than one isolate (e.g. ST3 was found in 6 isolates).
+You can find an example of MLST data correctly formatted [here](_images/sampleAPfile.txt). Note that in this file several STs are represented by more than one isolate (e.g. ST3 was found in 6 isolates).
 
-The Isolate data file can contain epidemiological and/or demographic data or any other data you want to visualize overlaid onto the results of the analysis algorithms. The link between the data in the two files is made by the Sequence Type identifier. You can find an example file correctly formatted [here](http://www.phyloviz.net/wiki/dataloading/sampleADfile.txt).
+The Isolate data file can contain epidemiological and/or demographic data or any other data you want to visualize overlaid onto the results of the analysis algorithms. The link between the data in the two files is made by the Sequence Type identifier. You can find an example file correctly formatted [here](_images/sampleADfile.txt).
 
 ## Loading a Dataset
 
 Go to _File_ menu and choose _Load Dataset_.
 
 If any errors in the data loading process are found they will be displayed in the session _Tab_. In the following screenshot you can see an example where allelic profiles were repeated with different identifiers. In the example data,we created ST81 as copy of ST1 profile and PHYLOViZ detects it and eliminates it from the analysis.
 
-![file menu](http://www.phyloviz.net/wiki/dataloading/LoadDataset.png)
+![file menu](_images/LoadDataset.png)
 
 The dialog will now guide the user in the loading of the data. The first step is choosing a name for your Dataset since now PHYLOViZ supports multiple datasets open simultaneously. You must also choose the Dataset Type from the dropbox menu.
 
 The Dataset type can be MLST or MLVA datasets with any number of loci, without any missing data. Lines with missing data will be excluded on load. If you have installed the Single Nucleotide Polymorphism (SNP) plugin, you can also access it on the Dataset type. See the [Sample Datasets](http://www.phyloviz.net/wiki/sampledatasets/) page to access some test data for the sequence-based typing methods available.
 
-![dataset type](http://www.phyloviz.net/wiki/dataloading/LoadDataSet_1.png)
+![dataset type](_images/LoadDataSet_1.png)
 
 The next step is loading the allelic profile data for the method you selected.
 
-![load profiles](http://www.phyloviz.net/wiki/dataloading/LoadDataSet_2.png)
+![load profiles](_images/LoadDataSet_2.png)
 
 After loading the allelic profile data, you can choose a file with information on your isolates for which the allelic profile was loaded. The linking field, as explained before, should be the Sequence Identifier and should be selected in the Key dropdown menu.
 
-![load isolates](http://www.phyloviz.net/wiki/dataloading/LoadDataSet_3.png)
+![load isolates](_images/LoadDataSet_3.png)
 
 Then the dataset is loaded and double clicking on the dataset name opens the available data.
 
-![open dataset](http://www.phyloviz.net/wiki/dataloading/DataSetloaded.png)
+![open dataset](_images/DataSetloaded.png)
 
 Double clicking on Isolate Data and Typing Data in the tree menu under the dataset name opens the respective tabs.
 
-![open isolates](http://www.phyloviz.net/wiki/dataloading/IsolateData.png)
+![open isolates](_images/IsolateData.png)
 
-![open data](http://www.phyloviz.net/wiki/dataloading/TypingData.png)
+![open data](_images/TypingData.png)
 
 The default view is the _table_ view. Also available is the tree view, where it is easier to visualize what information is available in the different fields and to select combinations of fields with specific values.
 
-![table view](http://www.phyloviz.net/wiki/dataloading/treeView.png)
+![table view](_images/treeView.png)
 
diff --git a/docs/querying_data.md b/docs/querying_data.md
@@ -6,13 +6,13 @@ The main goal of PHYLOViZ is to provide a data visualization tool for the users
 
 The _Isolate Data_ tab is displayed by double clicking on the _Isolate Data_ on the _Dataset_ tree. The following screenshot resumes the basic functionality of the display on the table view.
 
-![Isolate Data tab](http://www.phyloviz.net/wiki/queryvisualization/IsolateDataTable.png)
+![Isolate Data tab](_images/IsolateDataTable.png)
 
 ## The typing data tab
 
 The _Typing Data_ tab contains the allelic profiles loaded in the dataset. The name of displayed on the tab, and on the _Dataset_ tree, is the name of the selected method during the _Load Dataset_ procedure. The user can also query, select and visualize the data of the allelic profiles, similarly to operations describe in the Isolate Data tab. 
 
-![Typing Data tab](http://www.phyloviz.net/wiki/queryvisualization/TypingDataTable.png)
+![Typing Data tab](_images/TypingDataTable.png)
 
 ## Regular expression primer
 
@@ -29,7 +29,7 @@ Some basic regular expressions that can be used in PHYLOViZ. For more complex ex
 
 All these operators can be combined to create complex search expressions. For example : `^st[G|C].*6$` would find any field that starts with `st` followed by a `C` or a `G` then as 0 or more characters and ends with a `6`. The following screenshot shows the result on the test dataset:
 
-![REGEX example](http://www.phyloviz.net/wiki/queryvisualization/RegexExample.png)
+![REGEX example](_images/RegexExample.png)
 
 ## Queries using the table view
 
@@ -40,22 +40,22 @@ You can also automatically select multiple columns by clicking with the right mo
 Finally to plot the data on the Display tab, press the View button, after all the desired selections are performed.
 
 Click to see an example of querying:
-* [_Table_ view with selections](http://www.phyloviz.net/wiki/queryvisualization/TableViewRegex.png),
-* [query results Chart](http://www.phyloviz.net/wiki/queryvisualization/TableViewPie.png)
-* [results on _Display_ tab](http://www.phyloviz.net/wiki/queryvisualization/TVRdisplay.png)
+* [_Table_ view with selections](_images/TableViewRegex.png),
+* [query results Chart](_images/TableViewPie.png)
+* [results on _Display_ tab](_images/TVRdisplay.png)
 
 ## Queries using the tree view
 
 The _Tree_ view offers a faster way to create simple queries. The user can also use the regex filter to search the dataset but all the possibilities for each dataset column are automatically indexed in a tree like manner. By pressing the _Select_ button and switching to _Table_ view the user can see the resulting selection. The users can alternate both views (Table and Tree) at will for creating the selection.
 
-![Tree view with selections](http://www.phyloviz.net/wiki/queryvisualization/TreeViewSelections.png)
+![Tree view with selections](_images/TreeViewSelections.png)
 
-![Results on Display Tab](http://www.phyloviz.net/wiki/queryvisualization/TreeViewDisplay.png)
+![Results on Display Tab](_images/TreeViewDisplay.png)
 
 ## Exporting the results to an image file
 
 To export the resulting graphs to an image file. Click on the _Options_ button and choose _Export_. Select the adequate file format for the intended purpose. We recommend the use of png images for presentation quality and eps for publication quality.
 
-![Export](http://www.phyloviz.net/wiki/queryvisualization/Export.png)
+![Export](_images/Export.png)