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olga24912 committed Dec 10, 2019
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3.3. <a href="#sec3.3">Output</a><br>
3.4. <a href="#sec3.4">Example dataset</a><br>
4. <a href="#sec4">Visualization</a><br>
4.1. <a href="#sec4.1">Getting started</a><br>
4.2. <a href="#sec4.2">Genome browser layout</a><br>
4.3. <a href="#sec4.3">Free layout mode</a><br>
4.4. <a href="#sec4.4">Customizing visualization</a><br>
4.5. <a href="#sec4.5">Highlighting paths</a><br>
4.6. <a href="#sec4.6">Understanding visualization</a><br>
4.7. <a href="#sec4.7">Navigation</a><br>
5. <a href="#sec5">RNA-Seq scaffolder</a><br>
6. <a href="#sec6">References</a><br>
7. <a href="#sec7">Feedback and bug reports</a><br>
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<a name="sec3.1"></a>
## Command line options
## 3.1. Command line options
All input options are capable of taking only a single or a pair of files if specified. To provide multiple files use the same option again (e.g. `-c contigs1.fa -c contigs2.fa`). See more in the examples.

`-h` (or `--help`)
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e 1 3 1 0 32.5 200

<a name="sec3.2"></a>
## Command line examples
## 3.2. Command line examples

Let's say our dataset consists of:
- A set of contigs (`contigs.fa`)
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-o output_dir

<a name="sec3.3"></a>
## Output
## 3.3. Output

SGTK stores all output files in `<output_dir> `, which is set by the user.

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Open `main.html` in any browser to see visualisation. Chrome is preferred.

<a name="sec3.4"></a>
## Example dataset
## 3.4. Example dataset

SGTK comes with toy dataset, on which you can test your installation:

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<a name="sec4"></a>
# 4. Visualization
## Getting started

<a name="sec4.1"></a>
## 4.1. Getting started

After the graph is constructed and the web page is generated, you can open `main.html` in a web browser (we recommended to use Chrome, however it also was tested in FireFox, Opera and Safari).

![First step](https://raw.githubusercontent.com/olga24912/SGTK/master/resources/pic/firstStep.png)
Expand All @@ -369,14 +379,15 @@ SGTK has two layout modes: (i) free layout and (ii) genome browser. Free layout

![Layout](https://raw.githubusercontent.com/olga24912/SGTK/master/resources/pic/layout.png)

## Genome browser layout
<a name="sec4.2"></a>
## 4.2. Genome browser layout

In the genome browser mode, vertices of the scaffold graph are displayed as rectangles placed along the reference, lengths of which are proportional to the contigs sizes. Short nodes with adjacent edges are hidden and rendered only when zoomed in.

![Genome browser layout](https://raw.githubusercontent.com/olga24912/SGTK/master/resources/pic/genomeBrowserLayout.png)


## Free layout mode
<a name="sec4.3"></a>
## 4.3. Free layout mode

In case of free layout you can choose one of several filtration options. Once new visualization parameters are set, click the `DRAW` button and choose the component.

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## Customizing visualization
<a name="sec4.4"></a>
## 4.4. Customizing visualization

### Connection sources

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You can set up threshold for visualizing nodes. Note, that when visualizing nodes along scaffolds contigs shorter than the threshold still will be displayed.

## Path highlight
<a name="sec4.5"></a>
## 4.5. Highlighting paths

To ease the analysis, you can also highlight vertices, edges, paths and entire scaffolds.
To use this functionality, switch to highlight tab (top left).

![Default node](https://raw.githubusercontent.com/olga24912/SGTK/master/resources/pic/Highlight.png)

You can highlight vertex, edges, pathes and scaffolds.
Open highlight pan for doing that.

### Highlighted path description

#### Path description

![Default node](https://raw.githubusercontent.com/olga24912/SGTK/master/resources/pic/HighlightPathDescription.png)
To highlight a set of edges or vertices, one needs to specify them in the text box using simple description script.

You can write highlight description to that window.
There are following types of highlight description are currently supported:
* `scaffold_name` - scaffold name to highlight; will highlight all vertices and connections corresponding to this scaffold.
* `a` - contig name or contig id to highlight the corresponding vertex.
* `a --> b` - will find and highlight the shortest path between vertices a and b.
* `a -> b` - highlight vertices a and b and all connections between them.
* `a; b` - highlight vertices a and b without highlighting any connections between them.
* `a -eid> b` - highlight vertices a and b, as well as edge eid if it connects these two vertices.
* `a b` in this case the default connection type between vertices a and b will be used (see below).

There are following types of description:
* `scaffold_name` - scaffold name for highlight all vertex and connections corresponding to that scaffold.
* `a` - contig name or contig id to highlight vertex.
* `a --> b` - will be find and highlight the shortest path between vertices.
* `a -> b` - highlight contigs a and b and connections between them.
* `a; b` - highlight a and b indipendatly.
* `a -eid> b` - highlight contigs a, b and edge with eid if it connected this two vertices.
* `a b` in this case will be used default connection between contigs a and b.
Each vertex is specified by corresponding contig name or id.

a and b are contigs name or id.
![Default node](https://raw.githubusercontent.com/olga24912/SGTK/master/resources/pic/HighlightPathDescription.png)

#### Tapholding
#### Default connection

You can add vertex to the end of highlighting list by tapholding the vertex.
To choose the default connection type use the appropriate drop-down menu. Available types are: path, edge or none.

#### Default connection
![Default node](https://raw.githubusercontent.com/olga24912/SGTK/master/resources/pic/HighlightDefaultConnetction.png)

You can choose which connection will be use by default: path, edge or none.

### Fake edges
#### Extending highlighted paths

![Default node](https://raw.githubusercontent.com/olga24912/SGTK/master/resources/pic/HighlightFakeEdge.png)
To extend currently highlighted path, you can hold your left mouse button while pointing on the vertex of interest.

In case of edge or path absent fake connection between
two vertices will be red highlighting.

### Path extension
### Extending displayed component
If a path or a set of vertices/edges chosen to be highlighted is not entirely displayed in the current view, you will be prompted about extending the view and showing absent vertices.

![Default node](https://raw.githubusercontent.com/olga24912/SGTK/master/resources/pic/HighlightPathExtensionQuestion.png)

![Default node](https://raw.githubusercontent.com/olga24912/SGTK/master/resources/pic/HighlightPathExtension.png)

If the path not completely present on screen
you will be asked about showing absent vertices.
### Included sources

### Included connection sources

You can also choose which connection types will be highlighted.

![Default node](https://raw.githubusercontent.com/olga24912/SGTK/master/resources/pic/HighlightSourcesEx0.png)

![Default node](https://raw.githubusercontent.com/olga24912/SGTK/master/resources/pic/HighlightSourcesEx1.png)

![Default node](https://raw.githubusercontent.com/olga24912/SGTK/master/resources/pic/HighlightSourcesEx2.png)

You can choose which sources to take into account in path highlighting.

## Understanding visualization
### Missing edges

If a user asks to highlight an edge between two vertices that are not connected, a fake edge will be drawn between them and highlighted with red color (instead of typical blue highlight).
Such option can be useful, for example, when comparing scaffolds obtained with different methods.

![Default node](https://raw.githubusercontent.com/olga24912/SGTK/master/resources/pic/HighlightFakeEdge.png)



<a name="sec4.6"></a>
## 4.6. Understanding visualization

Below we provide brief information on how interprete SGTK visualization.

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## Navigation
<a name="sec4.7"></a>
## 4.7. Navigation

### View navigator

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