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