Automated labels layout

Skyline’s Relative Abundance and Volcano Plot graphs have ability to label the graph points and automatically layout the labels to avoid overlaps with data points and other labels.

User can use Formatting dialog to format and label series of peptide/protein points according to user-specified criteria. See DIA/SWATH data analysis tutorial (p. 27) for information on using the Volcano Plot formatting options. Also, selected peptides/proteins are labeled by default (the red color on the picture above).

The user can control label layout settings using graph’s context menu.

The Auto Arrange Labels menu item allows to turn automated label layout off (it is on by default). In this case the labels will be positioned immediately above the corresponding points disregarding possible overlaps, as shown on the image above.

When Auto Arrange Label is on, user can move the labels around to fine-tune the automatically generated layout. In Skyline version 24.1 label drag is enabled by moving the mouse over the label you want to move and pressing and holding Alt key. The mouse cursor will change to indicating the drag mode. In the later versions when the mouse is moved over a label, a label border box shows. When the mouse pointer is positioned over the border box it changes to and the label can be dragged.

By default the label layout is recalculated every time the graph is zoomed or panned, or the Skyline document is modified. This might make the graph a bit jumpy and hard to manage, especially when there is a lot of points/labels. Also any manual label re-positioning is lost. To avoid that you can use Suspend Label Layout context menu item. When the layout is suspended, Skyline would not recalculate the layout every time you zoom/pan the graph, but document edits, like peptide/protein addition/removal will still trigger it. So you might want to postpone the final fine-tuning until your document is stable.

The layout is saved in the *.sky.view file when you explicitly save the document. If you modify the labels layout without modifying the document structure and exit Skyline the layout changes will not be saved. Use Save toolbar button or menu item.