ArcDiagrams
We need to load some CT files (or other supported formats) from the user's computer that we can process with RNAStructViz. The required procedure is illustrated in the screenshot of the application main window shown below:
To compare two structures in the same arc diagram, they must have the same underlying base sequence. Generally, we think of a specific sequence as corresponding to a particular organism. The differences in structures corresponding to different pairing data from individual samples.
Select the organism you wish to analyze with RNAStructViz. RNAStructViz will automatically process the loaded input files and sort them into folders based on the underlying sequence base strands. We can select one of these folders by clicking the appropriate button on the lower-left of the image above. Once you have selected an organism by its folder, the right-hand side of the application is populated with the available CT structure file data. Note that, at any point, choosing a new organism on the left-hand-side, will allow you to consider graphical visualizations of a new set of loaded CT structures. The menu of new options is shown below:
Once you have the right-hand-side menu options displayed, click on the Diagram button at the top of the right-hand of the window.
This will bring up the separate Diagram Window which is depicted in the image below:
There are several key features of the Diagram Window:
- The three drop-down menus at the top of the window allow you to select up to three structures to draw and compare. Different colors automatically are assigned to arcs belonging to each subset of the selected structures. These colors are displayed below the drop-down menus. The colors used to highlight these features can be changed via user preferences.
- The Export PNG button at the upper right of the window allows you to save a copy of your current arc diagram for later reference or inclusion in papers or presentations.
- The zoom feature is activated by holding down the left mouse button and moving the mouse to enclose the rectangle you would like to magnify. The zoom feature resolution is discussed in our list of known limitations.