Plots a matrix of recombination frequencies between markers (S.J. Welham & D.A. Murray).
Options
DCHROMOSOMES = scalar, variate or text |
Specifies a subset of the linkage groups to be displayed |
|---|---|
TITLE = text |
General title for the plot |
WINDOW = scalar |
Window number for the graph; default 1 |
KEYWINDOW = scalar |
Window number for the key (zero for no key); default 2 |
PALETTE = string token |
Colour scheme for plot (colour, color, greyscale, grayscale); default colo |
Parameters
RECFREQUENCIES = symmetric matrices |
Recombination frequencies to plot |
|---|---|
CHROMOSOMES = factors |
Linkage group for each marker |
Description
DQRECOMBINATIONS plots the recombination frequencies between markers in a shade diagram. The RECFREQUENCIES parameter must specify the recombination frequencies, in a symmetric matrix with each row representing a marker. The linkage groups for each marker can be supplied, in a factor, using the CHROMOSOMES parameter.
The DCHROMOSOMES option allows you to display a subset of the linkage groups. The setting can be either a variate or a scalar referring to the levels of the CHROMOSOMES factor, or a text referring to its labels.
The TITLE, WINDOW, and KEYWINDOW options can specify a title, the plotting window, and the key window. The PALETTE option controls the colour scheme used in the shade diagram.
Options: DCHROMOSOMES, TITLE, WINDOW, KEYWINDOW, PALETTE.
Parameters: RECFREQUENCIES, CHROMOSOMES.
Action with RESTRICT
Restrictions are not allowed.
See also
Procedure: QRECOMBINATIONS.
Commands for: Statistical genetics and QTL estimation, Graphics.
Example
CAPTION 'DQRECOMBINATIONS example'; STYLE=meta
QIMPORT [POPULATION=F2] '%GENDIR%/Examples/F2maize_geno.txt';\
MKSCORES=mkscores; MKNAMES=mknames; PARENTS=parents
CALCULATE nmarkers = NVAL(mkscores)
CALCULATE ngenotypes = NVAL(mkscores[1])
QRECOMBINATIONS [POPULATION=F2; PLOT=*; USEPENALTY=yes] mkscores;\
NRECOMBINATIONS=TwopNrec; RECFREQUENCIES=TwopRecfreq;\
MKNAMES=mknames; PARENTS=parents
DQRECOMBINATIONS TwopRecfreq