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.