Color Scale Limits Dialog

Information


Gradient Style

The gradient style controls are used to select to use either a double gradient such as green-black-red or a single gradient such as black-red. The double gradient is most often used for two dye array systems in which the values are log2 ratios. In this case the mid-point is kept at 0.0 so that spots where the two channels have equal expression (log2(A/B) = 0) are depicted as black and spots where the expression is unequal will tend to be colored more toward the extremes. The double gradient might also be useful for single dye systems where a reference or median value is used to generate a log2(I/Ref).

The single gradient option is useful for single channel data where data falls over a continuum and there is no clear rationale to separate the data into two distinct color regions.

Color Range Selection

This section of the dialog is used to indicate the limits for the color scale and an optional "mid-point" value. The single gradient mode only requires endpoints while the double gradient mode provides for selection of a mid-point value. For two dye systems the mid-point should generally be left at zero so that spots with equal expression in the two channels are displayed as black.

Values that exceed the limits that are set will be displayed as the saturated endpoint color. The range of the data is given in parentheses next to the limit input boxes to assist in initial limit selections. The Update Limits button in this panel will apply the current limits to the display in MeV and will update the Color Saturation Statistics panel and Gradient and Limits Preview panel.

Color Saturation Statistics

This section of the dialog reports the number of elements that are beyond the limits defined by the color scale. These off-scale elements are displayed as the endpoint color of gradient closest to the element's value. The statistics are calculted using all spots that are not missing values and have not been filtered out of the main data set by an applied filter.

Limits and Gradient Preview

This panel presents the current gradient style and the selected range limits.