IGB User's Guide
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Changing graph appearance

Most graphs are drawn in graph tracks that are similar to the annotation tracks used to display annotations.  Floating graphs do not appear in such a track.  See  Floating graphs on page 58.

You can modify many properties of graph tracks in the same way you modify properties of annotation tracks.  Right-click on the track handle and choose from the menu.  See Customizing annotation tracks on page 37.

All graphs have a rectangular block drawn at the left-hand edge.  This is the graph handle.  It can be used to select floating graphs with the mouse.  For graphs that are drawn in a graph track, it is easier to select them by clicking on the track handle instead.

Settings and adjustments that are specific for graphs can be made using the Graph Adjuster tabbed panel.

To change the settings for one or more graphs that are displayed in IGB:

  • Click the Graph Adjuster tab.
  • Select the graph(s) to change by doing one of the following:
    • To change a single graph, click the colored bar at the left side of a graph (the graph handle) or the track label to select it.
    • Shift-click to select additional graphs.
    • To change the settings for all graphs that are currently displayed, click the Select All button in the Graph Adjuster panel.
  • Make changes to the graph settings by typing in new values or by operating sliders in the Graph Adjuster panel.  For details, see the sections that follow this procedure.

Any changes you make to the values in the Graph Adjuster panel will apply to all currently selected graphs.

Change the height of a graph

There are several ways to change the vertical height of a graph:

  • Select the graphs you want to change by clicking on their handles, then drag the Height slide bar in the Graph Adjuster tab.
  • If the graph is floating (see  Floating graphs on page 58), hold down the shift key and drag your mouse up or down on the colored bar at the left end of the graph.

Change graph styles

Graphs can be shown in various representational styles.  The type of graph that is most appropriate depends on the type of question being asked about the data.  For example, when comparing trends and patterns, it is very useful to use the line graph display method.  The number of expression intervals being shown also can affect the graph display choice.  The user is encouraged to experiment with the different display types to find out which method works best for specific purposes.

To change the graph style:

  • Click the colored bar at the left end of the graph to threshold.
  • Click the Graph Adjuster tab.
  • In the Style section choose one of the options.

The following graph styles are available in IGB:

  • Bar -- Individual values are shown as vertical bars that are one base wide for position graphs and of variable width for interval graphs.
  • Line -- Subsequent values are linked with a line.  Even if the input file was not sorted, the values will be connected in order along the genomic coordinate axis.
  • Dot -- Shows a single dot for each data value.  For interval graphs,  horizontal lines will be connect the start and end points.
  • Min/Max/Avg -- This is the default style for most graph data types and is usually fine for most purposes.  It is especially useful for showing very densely populated graphs with data points for large numbers of positions. 
    • When IGB is zoomed all the way in, the display is equivalent to the Bar style.  When zooming out, IGB starts to summarize values.  When the scale of the display reaches the point where individual x-values are associated with multiple score values, IGB picks the maximum and minimum values and draws a vertical bar between them.  In addition, IBG draws lines through the average of all the data points represented at each x value. 
  • Stairstep -- Similar to the bar graph style, except that bar widths along the horizontal axis are stair-stepped. 

For example, if position 100 has a value of 50 and position 200 has a value of 75 and there are no values in between, then IGB will draw a bar of height 50 that starts at position 100 and stops at position 200. Then, at position 200, IGB will draw a new bar of height 75 that terminates at the next location with a value.

This style is particularly useful for viewing .egr and .sgr files, ESTs, or other high-density data.

  • Heat map --  Instead of showing relative intensity via the height of the line at each pixel or coordinate as in most other graph styles, a heat map shows expression levels via color or brightness of the line at each pixel or coordinate.  This graph style is useful if you want areas of greater expression to jump out at you.  If a graph does not render or is hard to see, adjust the visible bounds of the graph until features are readily visible.  Several heat map color maps are available to choose from. Transparent color maps are available and may be useful for floating graphs.

The following image illustrates how a single data set would look in each of the graph styles.  The graph used for this image is a simple position graph.  An example of an interval graph was given in the introduction to this chapter.

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