Sample graphics from R/qtl

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Summary plot of experimental
  cross [69k] Summary plot for an experimental cross. The top left panel displays the pattern of missing genotype data; the top right shows the genetic map. The lower panels are histograms of two phenotypes.
Plot of missing genotypes [76k] Pattern of missing genotype data in a cross. Black pixels indicate missing genotypes. Gray pixels indicate partially missing genotypes (in an intercross, genotypes coded as "not B" or "not A").
Plot of genetic map [40k] Locations of markers on a genetic map.
Plot of comparison of two genetic
  maps [54k] Side-by-side comparison of two genetic maps. This can be useful for comparing the genetic map obtained from a database to that estimated with the observed data.
Plot of recombination fractions [110k] Estimated recombination fractions for all pairs of markers (on selected chromosomes), along with LOD scores for the test of r = 1/2. (The recombination fractions are in the upper left triangle; LOD scores are in the lower right triangle.) Red indicates a large LOD score or a small recombination fraction, while blue is the opposite. Note that a marker on chromosome 8 appears to be switched with a marker on chromosome 18. Further, a marker on chromosome 1 likely belongs on chromosome 18.
Plot of genotyping error LOD
  scores [23k] Genotyping error LOD scores. Colored pixels represent larger values of the error LOD scores described by Lincoln and Lander (1992) and which indicate likely genotyping errors. The genotypes corresponding to purple pixels are likely to be in error.
Plot of genotype data with
  potential errors flagged [48k] Observed marker genotype data for an intercross. White, gray and black circles correspond to the genotypes AA, AB, and BB, respectively. Genotypes flagged by red squares were indicated to be likely genotyping errors.
Plot of proportion of missing
  genotype information [32k] Proportion of missing genotype information, calculated in two ways (using the concepts of entropy and of variance). Values of 0 correspond to complete data; large values indicate regions with little marker data. The ticks below indicate the locations of genetic markers.
Plot of LOD curves from
  genome scan [34k] LOD curves for a single-QTL model for a selected set of chromosomes, calculated with the two-part model described by Boyartchuck et al. (2001), Nat Genet 27, 259-260. The ticks below indicate the locations of genetic markers.
Plot of LOD scores from
  two-dimensional, two-QTL genome scan [132k] LOD scores for a two-dimensional genome scan with a two-QTL model, for a selected set of chromosomes. Values in the lower right triangle are for joint two-locus LOD scores; values in the upper left triangle are LOD scores for the test of epistasis. The color scale at the right indicates separate scales for the joint LOD scores (right) and the epistasis LOD scores (left).

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