Settings
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## Settings

Java TreeView stores settings in a per-file manner. Thus, it is not possible to edit settings unless a file is loaded. Additionally, LinkedView stores many settings in a per-view manner. Specifically, only the url settings are document-wide; the rest are only per-view. Thus, you could have multiple dendrograms with different zoom and color settings, and multiple Karyoscopes with different averaging, all with the same underlying document.

### Url Settings

Figure 2.4. Url Settings Dialog

Url Settings allow you to select from one of the presets, or to directly edit the url string. There is a special substring of the url string, "HEADER", which is replaced by a partcular gene or url header which you select from the pulldown. The default is to either use the first column for a pcl, or the second column for a cdt. In the original Eisen layout, this is the YORF column.

There is also a checkbox which allows you to disable url linking entirely. Whether this box is checked initially is determined by the default url presets.

What exactly the url settings are used for depends on the view. Generally, clicking on a gene will cause the url for that gene to be loaded in an external browser.

### Dendrogram Font Settings

Figure 2.5. Dendrogram Font Settings Dialog

Choose the font used to render gene or array names and annotation.

### Dendrogram Pixel Settings

Figure 2.6. Dendrogram Pixel Settings Dialog

This fairly complicated dialog has three major parts. The first part allows you to set the pixel scaling for the global and zoom views. The second part allows you to set the contrast. The third part allows you to set the color settings for the dendroview.

The pixel scaling determines how tall and wide the boxes are in both the zoom and global views. Basically, the larger the pixel scaling, the bigger the box. If the pixel scaling is less than one, the rows are averaged. This can make your data look better, since missing values disappear.

The contrast is the expression value which corresponds to fully induced. Any values greater than this will appear to be the induced color, and values between this and zero will appear to be a color between the zero and up color. The contrast is similarly used to color repressed boxes.

The color part allows you to set the up, down, zero and missing colors. You can double-click the boxes to get a color selection dialog, click a preset to load a color, and load and store color sets to files.

In LinkedView, a dendrogram must be active in order for this option to appear on the settings menu. Any settings made only apply to the active dendrogram.

### Karyoscope Coordinates Settings

Figure 2.7. Karyoscope Settings Dialog

Coordinates may be parsed from the current file, if it is formatted properly, or parsed from an external file. The proper formatting is discussed in the File Formats section. The settings files provided with Java Treeview are nothing more than minimal PCL files, which contain no data but have annotation columns for chromosome, arm and position. The coordinates in an external files are matched up with the loci in the current file using either the first column, or if the first column has the header GID the second column. This gives the expected result when operating on PCL or CDT files, provided that the id column is unique.

Loci which do not have coordinates are not displayed. However, loci which have coordinates but not expression data associated with them do affect the extent of the chromosome displayed.

### Karyoscope Averaging Settings

Figure 2.8. Karyoscope Averaging Settings Dialog

Allows one to average genes with their genomic neighbors using one of several algortihms.

Karyoscope Averaging Methods

No Averaging

  Do not perform any averaging

Nearest

  Average the nearest k genes. The nearest may all be on one side; this method strictly finds the nearest.

Neighbor

  Average the (k-1)/2 genes on the left and the (k-1)/2 genes on the right together with this one. If there are fewer than (k-1)/2 genes on a side, then fewer genes are averaged.

Interval

  Average genes over an interval of k units. The unit is the unit which the coordinates of the genes are specified in. This is generally base pairs for the supplied coordinates files.

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