The Caryoscope Settings window is brought up when you select the menu item:
When you change a value, it is displayed with a "change bar" to the right, indicating that it has been changed but is not yet actively being used, and the and buttons become active:
The buttons at the bottom of the window function as follows:
Apply the currently modified setttings.
Cancel the changes made since the button was last pressed.
Change all the settings to the built-in Caryoscope default values. Use with care!
The thickness of the chromosome axis lines, in pixels. This allows you to tune the display to your preferences. It is best specified as a number less than 1, indicating a thin line. Here are a couple of examples:
| 0.5 | 1.0 |
|---|---|
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Whether the centromere is shown on the display. This is an unsupported feature at the moment and is considered a "work in progress".
Indicates whether the chromosome axis is shown as a vertical line.
| True | False |
|---|---|
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An expression for generating the feature tooltips. See Section 3.3.6, “Navigate Mode” and Section 3.6.1, “Expressions using annotations”. Below is an example:
An expression for generating the feature hyperlinks. See Section 3.3.6, “Navigate Mode” and Section 3.6.1, “Expressions using annotations”. Below is an example:
If logarithm computation is enabled, select the base of the logarithm function. See Section 3.5.1.1, “Logarithm calculation”.
Select whether the logarithm of the data values should be computed and shown. See Section 3.5.1.1, “Logarithm calculation”.
The minimum width, in pixels, along the chromosome axis, of the colored bar representing the data value associated with a feature. Use this to ensure that values which may be only a few base pairs wide are visible at any level of magnification. Note that you can specify a value less than 1 to indicate using a "thin" line. To disable this feature, specify a value of 0.0. Here are some examples:
| 0.0 | 0.5 | 1.0 |
|---|---|---|
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 |
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Select whether a moving average of the data values is computed and shown. See Section 3.5.1.2, “Moving average calculation”
Enter the "half decay distance" parameter of the moving average calculation. See Section 3.5.1.2, “Moving average calculation”
Enter the "half window width" parameter of the moving average calculation. See Section 3.5.1.2, “Moving average calculation”
The color to use for painting negative numerical values in datasets. In the examples shown here, negative values are painted in red.
The color to use for painting positive numerical values in datasets. In the examples shown here, negative values are painted in green.
The thickness of the data scale lines, in pixels. This allows you to tune the display to your preferences. It is best specified as a number less than 1, indicating a thin line.