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Plot Viewer

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12.2 Plot Viewer

The Plot Viewer is the viewer and control interface for all types of spreadsheet column plotting in SVS. It can be used to plot any numeric data column from the spreadsheet from which it was launched. A graph is one set of X- and Y-axes on which one or more sets of values are plotted. A graph item is any one set of X- and Y- coordinates plotted on a graph.

Within the same Plot Viewer window you can create one or more graphs each containing one or more items. All graphs share a common X-axis, though the Y-axes for all graphs are independent.

NOTE:

  • All new instances of the Plot Viewer create a new Navigator Window Node in the Project Navigator.
Navigating The Plot Viewer

On the Plot Viewer there are six regions to note and become familiar with: Plot Title Bar, Menu Bar, Tool Bar, Graph Control Interface, Data Console, Full Domain View, Graph View, and Annotation tracks (see Figure 88).

[Picture]

Figure 88: Plot Viewer Used as a Genome Browser

Plot Title Bar:

This contains the name of the plot as named in the Project Navigator Window, as well as the Navigator Window Node ID number in square brackets. See Project Navigator Window for more information.

Menu and Tool Bars

These contain the menus: File, View and Help.

The File menu contains the following items:

  • Save as Image: Opens the Save as Image preview window. See Saving Graphs to Image Formats for more information.
  • Save as PDF: Opens the Save as PDF preview window. See Saving Graphs to a PDF for more information.
  • Select Genome Map: Allows a different genome map to be selected. Genome maps could be for non-human species, a different human genome build, or a genome based on a spreadsheet of data. A genome map is defined by both the species and the build identifier. See Genome Maps.
  • Close: Closes the Plot Viewer after saving the current zoom and plot settings.

The View menu allows for the Plot Viewer subwindows to be turned on or off. A check mark in front of a subwindow indicates the window is shown, no check mark indicates it is hidden. A subwindow can be shown or hidden by selecting it from the list. The possible subwindows are:

  • Graph Control Interface: Displays graph and item tree structure, and sets graph and item parameters.
  • Full Domain View: Displays a full domain view of each graph, as well as the location of any zoom box.
  • Data Console: Displays information about data selected in the Graph View.
  • Annotation Tracks: Displays genome information tracks, if the X-axis is plotted on the genomic position scale.

The Help menu contains a link to the section in the SVS manual appropriate for the plot type.

The Tool Bar contains (from left to right) for:

  • Save as Image icon
  • Save as PDF icon
  • Print icon
  • (Genome Browser Only) Select Genome Map icon
  • Delete Navigator Node icon
  • Give Feedback icon
  • Show Project Viewer icon
  • Plot specific Help icon
  • (Genome Browser Only) Genome map and zoom selection options, see Features Unique to a Genome Browser
  • X-Axis Zoom selection, see Navigating The Plot Viewer

Tool Bar Controls for Non-Genome Browsers

Plot viewers that do not have a genome browser have X-axis zoom controls in the tool bar. The first text box is for the X-Min value, the second text box is for the X-Max value. These zoom controls are identical to the X-axis zoom controls found in the Graph control panel.

Graph Control Interface for Non-Genome Browsers

The Graph Control Interface has two components, User Graphs, and the Graph and Item settings control boxes. If the User Graphs node item is selected, then the Add Graph tab will be available. If a Graph name is highlighted in the Graph Control Tree, then the Graph tabs will be available. These tabs are usually: Graph, Axis and Add Item. Other tabs are available for special graph types. If an Item name is highlighted in the Graph Control Tree, then the Graph Item tabs will be available. These tabs vary depending on the graph item type.

The Graph Control Interface is described in Using the Graph Control Interface.

Data Console

The Data Console has three tabs:

  • Current: This tab displays information on the most recent point or histogram bar clicked in a graph or gene in the Genome Track. The information displayed depends on the type of graph and point clicked.
  • History: This tab displays information on all points, histogram bars, or genes clicked since the Plot Viewer was last opened.
  • User Annotations: Allows the user to save notes or document comments regarding the graphs in the Plot Viewer. These comments are saved when the Plot Viewer is closed and are available upon reopening of the Plot Viewer.

Full Domain View

The Full Domain View always shows the entire domain and range of each graph’s data in the Plot Viewer. The tabs at the top of the Full Domain View correspond to each graph. To switch to the Full Domain View of a different graph, click on the tab for that graph. If the domain of any graph is zoomed in, then on the Full Domain View, the visible portion will be highlighted in red. This red section is called the Zoom Box. If the the data is plotted as a Genome Browser, you can zoom in on a particular chromosome by double-clicking on the chromosome band in the Full Domain View. Double-clicking on a border between two chromosomes will zoom into the two adjacent chromosomes.

Graph View

The Graph View makes up the bulk of the Plot Viewer. If there are multiple graphs in the Plot Viewer, there is a minimum size enforced to prevent individual graphs from getting so small as to not be meaningful. In the case that there is more than one graph and both cannot be displayed simultaneously in their full size, a scroll bar will appear on the right of the Plot Viewer.

All graphs share a common X-axis, zooming in on the X-axis will change the independent axes for all graphs. The zoomed in section will be indicated by a red Zoom Box on each graph’s Full Domain View. See Zooming in the Graph View for more information on zooming in or out in the Graph View. Once zoomed in, you can pan along a graph’s Y-axis using the scroll bar at the right of the graph. Scrolling along the X-axis of all graphs is accomplished using the scroll bar at the bottom of the main graph window pane or the annotations window pane.

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