Plots a grid of marker scores for genotypes and indicates missing data (D.A. Murray).
||Type of plot (
||Lower genotype for the display|
||Upper genotype for the display|
||Specify a subset of the linkage groups to be displayed|
||Type of population (
||Colours to use for the different marker scores|
||Title for the graph|
||Marker score code for each marker|
||Linkage group for each marker|
||Labels to identify the parents|
DQMKSCORES produces graphical displays of marker scores for a set of genotypes. The marker scores should be supplied by setting the
MKSCORES parameter to a pointer containing to a set of factors (one for each marker). Each factor should have same labels, in the same order. The linkage groups for each marker are supplied in a factor by the
PLOT option controls the type of graph that is displayed:
||produces a shade plot where the genotypes are displayed using different colours, and|
||produces a shade plot displaying the missing marker genotypes.|
UPPERGENOTYPE options can be used to display a subset of genotypes, by supplying values for the lower and upper genotypes to be included in the plot.
DCHROMOSOMES option can be used 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 type of population must be specified using the
POPULATIONTYPE option. The following settings are available:
||first generation backcross population,|
||an F2 population,|
||population of recombinant inbred lines,|
||population of backcross inbred lines, and|
||data for association mapping.|
The parent information must be supplied using the
PARENTS parameter in a pointer to a set of texts. The first text in the pointer defines the alleles for parent 1, the second text defines the allele for parent 2, and so on. The labels for the parents are supplied in a text using the
COLOURS option can specify colours for the different marker scores. The colours can be supplied in a variate of RGB colours or in a text containing names of Genstat’s predefined colours (see
PEN). For a plot of the marker scores, the number of colours specified by the text or variate should match the number of different marker scores for the population, while for a missing-score plot they should represent those that are present, missing and partially missing (
BCxSy populations). For example, for a plot of the marker scores for a
DH1 population, three colours should be supplied for the scores 1/1, 2/2 and -/-. Similarly, for a missing genotype plot for a
DH1 population, two colours should be supplied to represent the present and missing scores.
TITLE option allows you to supply a title for the plot.
Any restrictions are ignored.
CAPTION 'DQMKSCORES example'; STYLE=meta QIMPORT [POPULATIONTYPE=F2] FILENAME='%GENDIR%/Examples/F2maize_geno.txt';\ MAPFILENAME='%GENDIR%/Examples/F2maize_map.txt';\ MKSCORES=mgenotypes; CHROMOSOMES=linkagegroups;\ PARENTS=mparents; IDPARENTS=midparents DQMKSCORES [PLOT=all; POPULATIONTYPE=F2] mgenotypes;\ CHROMOSOMES=linkagegroups; PARENTS=mparents; IDPARENTS=midparents DQMKSCORES [PLOT=missing; POPULATIONTYPE=F2] mgenotypes;\ CHROMOSOMES=linkagegroups; PARENTS=mparents; IDPARENTS=midparents