Vistories are a way to document an analysis you perform within SeqMonk. They are a report type which allows you to mix the automatic recording of events within the program (probe generation, filtering etc), with formatted text and embedded results such as graphs and tables. Vistories can be used to create a complete record of what you did in SeqMonk and then save it to an HTML document which you can archive or distribute to share your analysis with others.
A vistory is automatically created as soon as you start a project in SeqMonk and will start collecting automated events. To open up the report and start adding content to it just click on the large "V" icon on the toolbar, or by selecting Reports > Show Vistory from the main menu. You only have one vistory associated with each SeqMonk session and you can close and open the actual vistory window as often as you like without losing the content.
A vistory is composed of a series of blocks. Each block is of a specific type of content. The different kinds of content you can add to your vistory are:
When you first start a project, or re-open an existing project you will see a flurry of automated events as the various groups and replicate sets are created and the quantitation is defined. This can look a little messy, so rather than keep these as isolated events you can clear your vistory and insert a Project Summary. This adds a set of tables which summarise the current state of your project and serves as a good starting point for most analyses.
Any action which modifies the data stored in your project will trigger the automatic insertion of a data event into your vistory. Typical events would be:
These should collect enough information to allow you to replicate the actions which you used during your analysis.
Text input in a vistory comes in two types, titles and text. Titles can be of two levels (title and subtitle) and all can be inserted by pressing the appropriate buttons in the toolbar of the vistory.
Since it's common to add text after the analysis you can insert a title or text block at any point. You can select a block in a vistory by clicking on it and you should see a grey box appear around it. When you insert a title or text block it will insert below the selected block.
Title and text blocks can be moved after insertion. Just press the blue up or down arrows on the right of the block to move their position.
As well as showing a title and subtitle in your document, the titles and subtitles will also be used to build a navigation table of contents in your compiled document so it's a good idea to use these to structure your work
Within SeqMonk every graphical window which opens has the option to save the graphic. When you choose this you will be given the choice of whether to save it to a file, or to embedd it into your vistory. Graphics inserted into the vistory will appear exactly the same as when they were in the main program so it effectively takes a screen shot.
If the inserted graphic is too big to fit into the vistory window you can see the rest of it by clicking and dragging on the graphic to scroll it across the page. When exported into an HTML document large graphics will have scroll bars added to them.
Any table which can be saved (normally reports) can also now be embedded into a vistory. The table will appear directly in the report and will retain the ordering at the point where it was inserted.
Vistories are NOT saved along with the main SeqMonk project - they have their own files, and they can be loaded and saved independently of the main project.
You can save your vistory using the Save or SaveAs options in the vistory toolbar. You can also load in a previously saved vistory and this can either replace your current vistory, or be appended to the end of it.
You can create HTML reports from your vistory. These will be nicely formatted documents which you can read in a web browser. They contain all of the information in your vistory including all graphics and table data. Graphics are embedded into the HTML document so you can distribute just a single file. HTML documents can't be re-loaded into a vistory, so you should also use the save option to keep your analysis in an editable form.