Genotype Data Plots

Select menu: Stats | QTLs (linkage/Association) | Data Exploration | Genotypic Data | Genoytpe Data Plots

Use this to produce graphical displays of marker scores for a set of genotypes. A shade plot of all genotype scores or just the missing genotype scores can be displayed.

From the menu select
Stats | QTLs (linkage/Association) | Data Exploration | Genotypic Data | Genoytpe Data Plots.
Fill in the fields as required then click Run.

Available data

This lists data structures appropriate to the current input field. Double-click a name to copy it to the current input field or type the name. If data has been stored in a QTL data space then only the data structures present within that data space will be displayed in the Available data, otherwise all the current data within Genstat will be displayed. When data are present within the QTL data space you can right-click on the Available data list to open a shortcut menu where you can change between displaying data only within the data space and all data within Genstat.

Marker scores

A pointer specifying the marker scores. The pointer should contain a set of factors (one for each marker) where each factor contains the labels for the alleles separated by the ‘/’ character. For example, if the allele for parent 1 was a and the allele for parent 2 was b the labels for a factor for a marker should be as follows:

a/a, b/b, -/-	For a doubled haploid population.
a/a, a/b, -/-	For a backcross population.
a/a, b/b, a/b, a/-, b/-, -/-	For a F2, recombinant inbred line or backcross inbred line population.

where – = missing. The parent information for each marker should be supplied using the Parental information field.

Linkage groups

A factor defining the different linkage groups (or chromosomes).

Parental information

For an F2, DH, RIL, BCxSy or BC1 population this specifies a pointer to a set of texts (one for each parent) containing the parent information.

Labels for parents

For an F2, DH, RIL, BCxSy or BC1 population this specifies a text containing id labels for the parental information.

Type of population

A list of population types. Select as follows:

F2 for an F2 population
BC1 for a backcross population
DH1 for a double-haploid population
RILn for a population of recombinant inbred lines
BCxSy for a population of backcrossed inbred lines
Association mapping for an association mapping population.

Display

This specifies the type of shade plot that is produced and aspects of the display.

All genotype scores	Produces a shade plot with each of the marker scores in a different colour.
All missing scores	Produces a shade plot showing the missing genotype scores.
Lower genotype	Specifies the lower genotype to use in the display.
Upper genotype	Specifies the upper genotype to use in the display.
Subset linkage groups	Defines a subset of the linkage groups to use in the plot. This can be set to variate or a scalar of the group number(s) defining a subset of the levels of the linkage groups factor. If the linkage groups factor contains labels then a text defining a subset of its labels can be supplied. Alternatively, a comma separated list of group number(s) or labels can be supplied to specify the subset of linkage groups

Action buttons

Run	Create the shade plot.
Cancel	Close the dialog without further changes.
Defaults	Reset options to the default settings. Clicking the right mouse on this button produces a shortcut menu where you can choose to set the options using the currently stored defaults or the Genstat default settings.
Colours	Opens a dialog where you can customize the colours used in the different plots.

Action Icons

	Pin	Controls whether to keep the dialog open when you click Run. When the pin is down the dialog will remain open, otherwise when the pin is up the dialog will close.
	Restore	Restore names into edit fields and default settings.
	Clear	Clear all fields and list boxes.
	Help	Open the Help topic for this dialog.