Plots the results of a genome-wide scan for QTL effects in multi-environment trials (M.P. Boer & J.T.N.M. Thissen).
||Type of population (
||Method to be used for plotting (
||Threshold value for test statistic; default 0|
||Allows a subset chromosomes to be specified to display; default
||Whether to suppress the vertical lines between the chromosomes (
||Defines the plotting symbol for each point, as in the
||Multiplier used in the calculation of sizes of symbols when
||Whether to draw the outer line the
||Colours to use for the chromosomes; default
||Title for the y-axis of the lower graph; default
||Title for the y-axis of the upper graph; default uses the identifier of the
||Title for the x-axis; default
||Upper bound for y-axis of the upper graph|
||Whether to include annotation of the effects in the plot (
||Test statistics to be plotted; must be set|
||Chromosome for each locus; must be set|
||Positions on the chromosome of each locus; must be set|
||QTL effects in the different environments; must be set|
||Standard errors of the QTL effects in the different environments; must be set|
||Labels for the different environments; must be set|
||Labels to use to identify the effects|
||Labels to use to identify the parents|
||Name of the graphics file for the plots|
DQMQTLSCAN plots QTL × E effects which can be calculated by the
QMQTLSCAN procedure. The population type must be set by the
POPULATIONTYPE option, and the chromosome numbers and positions on the chromosome of the loci must be specified by
POSITIONS parameters respectively. The plot consists of 2 parts: in the upper part the test statistic specified by parameter
STATISTICS is plotted against the position of the QTL on each chromosome. If you also want to include the QTL main effects in the plot, you can set the
STATISTICS parameter to a pointer with 2 variates. The second variate is then plotted, in blue, in the upper part of the screen. A horizontal red line is drawn at the threshold specified by the
In the lower part of the screen, the effects of the different environments, supplied by the
QEFFECTS parameter, are displayed by plotting squares of different colours for significant loci (assessed at the 0.05 level, using the standard errors supplied by the
QSE parameter). There can be one, two or three plots here, according to the length of the
QSE pointers. Titles for the plots can be supplied by the
IDEFFECTS parameter. The first element of the
QSE pointers supplies the additive effects and their standard errors. These are plotted with bluish colours for parent 1 and yellowish colours for parent 2. Their second elements can supply the dominance effects, which are plotted with bluish colours for negative effects and yellowish colours for positive effects. Their third elements can supply additive 2 effects, which are plotted with bluish colours used for parent 3 and yellowish colours for parent 4. By default, this information is appended to the title, together with labels of the parents supplied by the
IDPARENTS parameter. However, you can set option
ANNOTATION=omit to omit it. The brightness of the colours indicates the significance of the effects.
STATISTICS parameter is set to a variate (or a pointer of length 1), the
METHOD option specifies the type of plot: either a line plot, a Manhattan (i.e. point) plot or spikes. The default is a line plot (and this is the only method available when the
STATISTICS parameter is set to a pointer of length 2). The Manhattan plot is a point plot with a different colour for each chromosome. The colours to use for the chromosomes are specified by the
COLOURS option using either a text of colour names or a variate of RGB values (see the
PEN directive for details). If
COLOURS is not set, the default is to use the default colours of the pens 1, 2, onwards, up to the number of chromosomes. The
SUPPRESSLINES option allows you to suppress the vertical lines that are drawn between the chromosomes. Options
BLACKOUTLINE are relevant only to Manhattan plots.
SYMBOL can be set to a scalar containing the number of one of the pre-defined plotting symbols (see the
SYMBOL parameter of
PEN). The default value 2 gives a circle, 5 gives a square, 6 gives a diamond, 7 gives a triangle, and 8 gives a nabla.
SIZEMULTIPLIER specifies scalar defining the multiplier to use in the calculation of the size of the symbols; default 1.
BLACKOUTLINE can be set to
yes to draw outlines of the symbols in black.
DCHROMOSOMES option allows you to specify a subset of chromosomes to plot. These are identified using either the levels or the labels of the
CHROMOSOMES factor. By default,
DCHROMOSOMES is not set, all the chromosomes are plotted.
TITLE option can provide an overall title for the plot in the upper graph. The
YLOWERTITLE option specifies the title for the y-axis in the lower graph; default
YUPPERTITLE option specifies the title for the y-axis in the lower graph; the default uses the identifier of the
STATISTICS variate. The
ENVNAMES parameter is used to label the other lines along the y-axis of the lower graph. The upper bound of the y-axis in the upper graph can be specified by the
By default, the plot is sent to the screen. However, you can supply a file for the plot, using the
DFILENAME parameter. You can discover the types of graphics file that are supported by running the command
Restrictions are not allowed.
CAPTION 'DQMQTLSCAN example'; STYLE=meta SPLOAD '%GENDIR%/Examples/F2maizemarkers.gwb'; SHEET='LOCI' SPLOAD '%GENDIR%/Examples/F2maize_multi_out.gwb' SCALAR thres; VALUE=3.21 "from QMQTLSCAN" TEXT [VALUES=IS94a,SS94a,HN96b,LN96b,LN96a,IS92a,NS92a,SS92a] LabEnv DQMQTLSCAN [POPULATIONTYPE=F2; THRESHOLD=thres; TITLE='YIELD';\ METHOD=line] STATISTICS=minlog10p; CHROMOSOMES=mkchr;\ POSITIONS=mkpos; QEFFECTS=Eff2; QSE=Se2; ENVNAMES=LabEnv DQMQTLSCAN [POPULATIONTYPE=F2; THRESHOLD=thres; TITLE='YIELD';\ METHOD=manhattan] STATISTICS=minlog10p; CHROMOSOMES=mkchr;\ POSITIONS=mkpos; QEFFECTS=Eff2; QSE=Se2; ENVNAMES=LabEnv DQMQTLSCAN [POPULATIONTYPE=F2; THRESHOLD=thres; DCHROMOSOMES=1;\ METHOD=line; TITLE='YIELD'] \ STATISTICS=minlog10p; CHROMOSOMES=mkchr;\ POSITIONS=mkpos; QEFFECTS=Eff2; QSE=Se2; ENVNAMES=LabEnv DQMQTLSCAN [POPULATIONTYPE=F2; THRESHOLD=thres; DCHROMOSOMES=!(1,9);\ METHOD=spikes; ; TITLE='YIELD']\ STATISTICS=minlog10p; CHROMOSOMES=mkchr;\ POSITIONS=mkpos; QEFFECTS=Eff2; QSE=Se2; ENVNAMES=LabEnv;\ IDEFFECTS=!t(Additive,Dominance)