Color gradient

To display properties on molecular surfaces, two different approaches are applied. One method assigns color codes to each grid point of the surface. The grid points are connected to lines chicken-wire) or to surfaces (solid sphere) and then the color values are interpolated onto a color gradient [200]. The second method projects colored textures onto the surface [202, 203] and is mostly used to display such properties as electrostatic potentials, polarizability, hydrophobidty, and spin density. 

Figure 20.11 Coverage of protein ErbB2 by shotgun proteomic discovery of sample fixed for various times, including fresh. The color gradient represents the increasing abundance of the peptides. All were identified at an FDR <1%. Reproduced with permission from Reference 20.

Let us now consider the case of varying illumination. A color gradient is applied to the original Mondrian image such that the color at the starting point of the path on the first... 

Figure 7.3 Mondrian image with color gradient. The color gradient was chosen such that the color of the first point of the path is equivalent to the color of the second point of the path.

Land (1983) reports that the viewed image can be surprisingly far out of focus without an impact on color perception. However, in this case a sharp color edge turns into a smooth color gradient. It therefore seems unlikely that human color perception uses some type of threshold. Also, Marr (1982) notes that one is able to see a rainbow. If the retinex algorithm were used by the visual system, one would assume that the rainbow were thresholded out because a rainbow is a smooth transition of all colors of the spectrum. 

Both the GET and POST methods accept KEGG identifiers as input and colors in hexadecimal code (hex code) format for fore- and background color. The usage of hex code for colors allows use of color gradients for mapping of differential gene expression or different metabolite concentrations. 

Figure 8. Predicted and observed color gradients for some field elliptical galaxies. From Menan-teau et al. (2001).Figure shows from left to right /si4-band surface brightness map, V606- 8i4 color pixel map and V606--l8i4(r) color gradient. Open circles represent observed gradients while solid lines are the model predictions obtained by means of the Martinelli et al. (1998) model.

Each pixel in the heatmap is colored, where a color gradient scale is used to represent gene expression intensity. Typically green to red, or more recently blue to yellow, is used to represent increasing gene expression. These plots are effective visualizations and have been widely used in microarray literature. These plots are often referred to as Eisen plots. 

Fig. 1. Modular organization of polymerases in different families. The modular organization of the five Escherichia coli and 16 human polymerases is shown with the number of amino acid residues in each polypeptide, as indicated. The polymerase domains are colored red, and other domains or functional motifs are color coded as indicated in the legend. A color gradient is used (see Pol III) to indicate that the domain boundaries are not defined. (See Color Insert.)...

The color gradient in Figure 4 denotes the percent actives (w/v) of NaCI at each composition studied. The salt concentrations range from -0.5% to very low concentrations, near 0.0% actives. 

FIGURE 9.5 Random forest-based QSPR model for the prediction of melting points. Additionally, the nnmher of ring bonds and second o-moment (M2) are shown via point size and color gradient, respectively, see insert for color representation of the figure.)... 

When specimens have nonuniform surfaces, repositioning them will usually result in different measurements. Recording exactly what position was measured, what viewing conditions (instrument geometry) were used, and what limitations should be expected if the measurement should be repeated should be considered part of the run data. Sometimes the nature of a color gradient is the point of a measurement— for example, colors of variable thickness films, some paint drawdowns with substandard hiding power, and... 

Figure 7.17 plots the results of the interfacial temperature analysis. The color gradient represents the difference between the calculated interfacial temperature and the bulk liquid temperature from SD4. This temperature difference is plotted as a function of the pressure at the screen and bulk liquid temperature inside the test tank. A positive value indicates that the interfacial temperature has warmed up relative to the bulk liquid, while a negative value indicates cooler interface temperatures relative to the bulk liquid. 

Figure 1.9 A parallelepiped body in its pristine (top panel) and shear-deformed (bottom panel) form. The force, Fq, is applied parallel to the top surface of area A (= length along x times thickness along z). In the bottom scheme the linear color gradient exemplifies the velocity gradient (red lower velocity, white higher velocity), vJH, which is also indicated by arrows of length increasing along y.

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