Figure 1.
Textile plots of simulated two SNP genotype data.
(a) The plot corresponds to the contingency table (Table 1) whose marginal genotype counts are shown by each circle with area which is proportional to the number of replicates, and each pairwise count of the two genotypes is shown by the width of a segment connecting two genotypes. (b) The column indicates the difference of the covariance
and the row indicates different pair of allele frequencies
. The greater the grade of the line crossings between two SNPs, the weaker the covariance between the SNPs. We also see that the steeper the slope between heterozygotes, the greater the allele frequency difference between A and B.
Table 1.
Simulated data for two SNP loci.
Figure 2.
Textile plots and pariwise LD displays for simulated data.
(a) Textile plot shows LD between adjacent SNPs by means of crossing lines which tend to increase if the adjacent SNPs are in linkage equilibrium (LE) and decrease in LD. (b) Textile plot shows the absolute and complete LD by specific geometrical shapes. There exist the absolute LD between 1st and 2nd SNPs and the complete LD between 2nd and 3rd SNPs in contrast to the LE between 3rd and 4th SNPs. (c) Pairwise (left) and
(right) displays of the same data shown in (a). (d) Pairwise
(left) and
(right) displays of the same data shown in (b).
Figure 3.
Textile plots and pairwise LD displays of 8 SNPs located in the region 29,933–30,112Kb on chromosome 6.
(a) There exist two absolute LD blocks composed of the first 4 SNPs and the last 4 SNPs, and the 8 SNPs comprise a complete LD block as a whole. (b) The and
displays. (c) Homozygous pairs of major haplotypes AAGAAAAG, GGAGAAAG and GGAGCGGA are highlighted. (d) Heterozygous pairs of the major and a few minor haplotypes are highlighted.
Figure 4.
The textile plot of 3,736 SNPs (within 22,009,637–39,115,518 on chromosome 6) located in a region surrounding Major Histocompatibility Complex (MHC) region.
It clearly shows the existence of very long range LD which covers the whole MHC region (the long range LD block can also be confirmed in the pairwise LD display based on the correlation coefficient in Figure S2.
Figure 5.
Textile plots and pairwise LD displays of SNPs located in a region surrounding HLA-DP genes, including the disease-susceptibility SNPs rs3077 and rs9277535 for the chronic hepatitis B.
(a) The order of SNPs was according to the physical order on chromosome 6. The leftmost axis indicates the affection status for the chronic hepatitis B cases (BCH), and the controls (CTRL). (b) The order was rearranged by the heuristic clustering algorithm described in Methods. The affection status was not included in the clustering algorithm. (c) Pairwise (top) and
(bottom) displays. (d) The top 3 frequent homozygote stretches in HLA-DP region are highlighted.
Figure 6.
Textile plots of 14 SNPs surrounding LCT gene on chromosome 2 for the seven ethnic groups from HapMap data.
Each of the four panels shows the plot of a specific population(s) indicated by the leftmost axis.
Figure 7.
Degree of horizontalness in the textile plot.
The polygonal line specified by shows the observation for
th individual, and horizontal line specified by
is the ideal coordinate for
th individual. The squared sum of Euclidean distance between the polygonal line and the horizontal line on each axis is minimized for all individuals simultaneously.