LEM: Customization
Parameter Information
Customization parameters are used to control scaling of arrows
that represent loci and the scaling of unsampled or intergenic
regions. These parameters can help constrain the length of an
open (unsampled) regions or long loci.
Locus Arrow Dimensions
These options control the rendering of locus arrows. Use Fixed
Arrow Length indicates that all loci should appear to be of the
same length as indicated by the text field. The input units are pixels and
at any point the Preview button can be hit to see the
impact of the current settings. Using fixed length arrows helps to
constrain the size of the viewer and fit more loci into a viewable
area.
The Use Scaled Arrow Length option will scale arrows such
that each pixel corresponds
to a given number of bases. The Scaling Factor controls the scaling
by applying a supplied factor in units of bases/pixel. Decreasing
this factor increases the length of the arrows and the resolution of sequence
length differences by rendering fewer bases per pixel length.
The Minimum and Maximum Scaled Arrow Length parameters constrain
the redering
so that very short sequences are rendered such that annotation can be
read and very long sequences are not unreasonably long. Regardless of the
scaling, the 5' and 3' ends of the locus are always provided as
annotation.
Intergenic or Unsampled Region Dimensions
This option allows you to cotrol the length of unsampled areas of
the chromosome. Using a fixed length constrains all areas not covered
by a sampled locus to be constrained to 1 pixel. This compresses areas
that might be quite long and uninformative if sampled loci are spread far appart.
If the fixed length option is not selected there is a parameter to constrain
the length of these areas to fall below a supplied limit.
Locus Replicate Rendering
This option displays an arrow for each spot that corresponds to a given locus.
If four spots map to a locus then one arrow is displayed for the mean expression
and four arrows are shown to the right that correspond to the expression of
each of the four spots. If selected, arrow and unsampled regions are both
moved to the fixed option to simplify rendering of the replicate arrows.