Contoured scatterplot

Fig. 13. The strategy used for the construction of contoured scatterplots. Positions of metal ions near a carboxyl group are plotted for different crystal structures. The result is a scatterplot. Gaussian peaks are put on each scatterplot point. The resulting density is contoured as for an electron density. The result is a plot of the orientational preferences for binding.

The contoured scatterplots showed that the most likely arrangements of metal cations are those designated syn, anti, and direct. The percentages of directionalities of metal liganding for a total of 1558 metal-carboxylate interactions are 62.9% syn, 22.7% anti, and 14.4% direct. Minimum metal ion-ligand distances are given in Table IX(a). syn is generally preferred, except when the distances are short... 

Fig. 7. (a and b) Two perpendicular orientations of a scatterplot of 108 unique and independent phosphinyl-metal ion interactions. Orientation (a) represents the phosphinyl group as in Fig. 6. Contours indicate where interactions tend to cluster, and syn coordination stereochemistry is preferred by 63%.

Lowess normalization methods are based on lowess (loess) scatterplot smoothing algorithms. The lowess smoother attempts to smooth contours within a dataset. Typically the lowess will be robust to genes which are active in treatment as they will be observed as outliers (45). Some normalization methods include a print-tip normalization (46), since physical location on the array and the print-tip may contribute some effect and variance beyond the biological and treatment variation. 

FIGURE 3.5 Scatterplots (a) of a bivariate normal distribution (100 points) with a correlation of 0.75, S = 0.44. Ellipses are drawn at 80 and 95% confidence intervals. Contour plots (b) and mesh plots (c) of the corresponding bivariate normal distribution functions are also shown. 

Figure 5. Thermal - (radians) scatterplots for terminally blocked valine at T = 0.2 kcal/ mol (a, d), 0.6 kcal/mol (b, e), and 2.2 kcal/mol (c,f) and the corresponding descriptions produced by the angular linear quasi-harmonic (a-c) and multivariate wrapped Gaussian (d-f) models. The shaded regions are bounded by the contours where ( , )/ ( 0, °) = e 2. In contrast to the quasi-harmonic method, the MWG method accurately models the data set even at high temperatures. (Adapted from Church and Shalloway [38].)...

Figure 4 IsoStar scatterplots of an N-H contact group around an amide central group (a) standard plot (all contacting N-H bonds shown) and (b) contoured plot.

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