Displays a genetic map (D.A. Murray).
Options
ORIENTATION = string token |
Orientation of map (vertical, horizontal); default vert |
|---|---|
DCHROMOSOMES = variate, text or scalar |
To specify a subset of the linkage groups to be displayed |
TITLE = text |
General title; default * |
Parameters
CHROMOSOMES = factors |
Factor defining the linkage groups |
|---|---|
POSITIONS = variates or pointers |
Positions of markers within the linkage groups |
MKNAMES = texts |
Names of the markers |
QCHROMOSOMES = factors |
Factor defining the linkage groups of the QTLs |
QPOSITIONS = variates |
Positions of QTLs within the linkage groups |
QNAMES = texts |
Names of the QTLs |
QINTERACTIONS = variates |
Logical variate indicating whether the QTL has significant (1) or non-significant (0) QTL-by-environment interaction |
Description
DQMAP plots a genetic map of marker locations within linkage groups. The linkage groups are supplied in a factor by the CHROMOSOMES parameter. The positions within the linkage groups are supplied by the POSITIONS parameter in a variate or in a pointer of 2 variates; if a pointer is supplied, the positions of the same marker are connected by a straight line. The names of the markers can be supplied in a text using the MKNAMES parameter. In the Graphics viewer in Genstat for Windows, the marker names can be viewed using the Data Info tool.
QTLs can be displayed on the plot by supplying the linkage groups of the QTLs in a factor using the QCHROMOSOMES parameter, and the positions within the linkage groups in a variate using the QPOSITIONS parameter. The names for the QTLs can be supplied in a text using the QNAMES parameter. If no names are supplied, the QTLs will be labelled using Q1, Q2 and so on. When displaying QTLs from a multiple environment analysis, the QINTERACTIONS parameter can be used to supply a logical variate indicating whether the QTL has significant (1) or non-significant (0) QTL-by-environment interactions. The QTLs identified as having QTL-by-environment interactions will then be displayed in a different colour.
The DCHROMOSOMES option can be used to display a subset of the linkage groups. The setting can be either a variate or a scalar of the group number defining a subset of the levels of the CHROMOSOMES factor, or a text defining a subset of its labels. The ORIENTATION option controls whether the map is plotted vertically (the default) or horizontally.
The TITLE option can be used to provide a title for the graph.
Options: ORIENTATION, DCHROMOSOMES, TITLE.
Parameters: CHROMOSOMES, POSITIONS, MKNAMES, QCHROMOSOMES, QPOSITIONS, QNAMES, QINTERACTIONS.
Action with RESTRICT
Any restrictions will be ignored.
See also
Procedures: DQMKSCORES, DQMQTLSCAN, DQSQTLSCAN, QMKDIAGNOSTICS.
Commands for: Statistical genetics and QTL estimation, Graphics.
Example
CAPTION 'DQMAP example'; STYLE=meta
QIMPORT [POPULATION=F2]\
'%GENDIR%/Examples/F2maize_geno.txt';\
MAPFILE='%GENDIR%/Examples/F2maize_map.txt';\
MKSCORES=mkscores; MKNAMES=mknames; PARENTS=parents;\
CHROMOSOMES=mkchr; POSITIONS=mkpos
DQMAP CHROMOSOMES=mkchr; POSITIONS=mkpos; MKNAMES=mknames
QMAP [PRINT=summary,map; PLOT=map; POPULATION=F2;\
SPATIAL=sampling]\
MKSCORES=mkscores; MKNAMES=mknames; PARENTS=parents;\
CHROMOSOMES=mkchr; SPOSITIONS=mkposnew; SEED=234098
DQMAP CHROMOSOMES=mkchr; POSITIONS=!p(mkpos,mkposnew); MKNAMES=mknames
DQMAP [DCHROMOSOMES=!(2,3,5); ORIENTATION=horizontal]\
CHROMOSOMES=mkchr; POSITIONS=mkpos; MKNAMES=mknames
QMAP [PRINT=summary,map; PLOT=map; POPULATION=F2;\
SPATIAL=sampling; MAPCHROMOSOMES=!(2,3,5)]\
MKSCORES=mkscores; MKNAMES=mknames; PARENTS=parents;\
CHROMOSOMES=mkchr; SPOSITIONS=submkposnew; SEED=128174
SUBSET [CONDITION=mkchr.IN.!(2,3,5); SETLEVELS=yes] mkchr,mkpos,mknames;\
submkchr,submkpos,submknam
DQMAP CHROMOSOMES=submkchr; POSITIONS=!p(submkpos,submkposnew);\
MKNAMES=submknam