Genome Browser graph-based tracks may be
a variety of ways to highlight different aspects
of the displayed information. Some track types,
such as BAM tracks and certain gene tracks, offer dynamic
calculation of items in the current window to
display a density graph where the height is
proportional to the number of items mapped to
each genomic position. The following
information explains each of the available
The default "transparent" setting
displays the colored transparent graphs of
multiple subtracks overlayed in the same
vertical space. The "solid" setting
displays the colored opaque graphs of multiple
subtracks overlayed in the same vertical space.
The "stacked" setting displays each
graph stacked on top of each other where the
high point of the graph is the sum of
all the values.
The "none" setting displays each
graph in its own vertical space. Note that not
all graph-based tracks include this option.
Type of graph: The default
"Bar" setting depicts the graph
data using color-filled bars. To view the data as
a series of points or lines, select the
Track height: To change the default display
height of the graph in pixels, type in a value
from within the indicated range.
Vertical viewing range: The min and max
values specify the vertical portion of the graph
that is displayed (default range is 30-70). These
numbers can be used to set data threshold
indicators. For example, to display only those
GC values greater than 50 percent, set the min
value to "50".
Data view scaling: The default "Use
vertical viewing range setting" option
displays the data using the parameters specified
in the Vertical viewing range setting. To
configure the graph to automatically scale to a
range defined by the minimum and maximum data
points in the current view, select the
"Auto-scale to data view" option.
To keep the y=0 value in view at all times when
Auto-scale is selected, set "Always
include zero" to "ON".
Transforms the data points by the function selected
in the drop-down menu. Usually the default
setting is "None".
Windowing function: When a view is too
large to show individual data values, the values
must be combined to produce a plot point. This
option specifies the combining function to be
used (default is "Mean"):
"Mean+whiskers" - displays the mean in a
dark shade, one standard deviation around the mean
in a medium shade, and the maximum/minimum in a light
shade. For bar graphs only the mean, the mean plus
a standard deviation, and the max are visible.
This mode is not available if the Overlay method is stacked.
"Maximum" - displays the maximum value of all
the points to be combined
"Mean" - displays the mean
"Minimum" - displays the minimum of all the
points to be combined
Smoothing window: When set to a numerical
value, this option determines the size, in pixels,
of a smoothing window to be passed over the plot
to smooth the edges of the bars or lines. This
is equivalent to a trend line calculation on the
graph. The default setting is "OFF".
Negate values: When checked, all values in the wiggle are negated, meaning that positive values become negative and vice-versa. This is useful for wiggles representing transcription or other activities on the Crick strand. Be aware that wiggles with negative values are drawn in altColor not color as positive values are.
Draw indicator lines:
Select the "ON" setting to display a
line marking the 0.0 position on the graph
(default is "OFF").
at y= :
Select the "ON" setting to display a
line on the graph at the specified numerical value
(defaults are "0" and "OFF").
This line can be used to mark a significant
threshold on the graph.
When you have finished making your configuration
changes, click the Submit button to
return to the annotation track display page.