Plots the results of a genome-wide scan for QTL effects in single-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; default uses the identifier of the
||Title for the x-axis; default
||Upper bound for y-axis|
||Window number for the graphs; default 1|
||Window number for key (zero for none); default 2|
||Whether to clear the screen before displaying the graph (
||Test statistic(s) to be plotted; must be set|
||Chromosome for each locus; must be set|
||Position on the chromosome for each locus; must be set|
||QTL effects along the genome,|
||Standard errors of the QTL effects|
||Labels along the x-axis to identify the effects when
||Labels to use to identify the parents|
||Name of the graphics file for the plots|
DQSQTLSCAN plots the results of a genome-wide QTL search which can be calculated by the
QSQTLSCAN procedure. The positions on the chromosomes where a test for the presence of a QTL has been performed must be given by the
POSITIONS parameter and the corresponding chromosome number by the
CHROMOSOMES parameter. The values of the test statistic must be set by
STATISTICS parameter, and the threshold by
THRESHOLD parameter. It is also possible to plot a second test statistic in the graph by setting the
STATISTICS parameter to a pointer containing two variates.
QEFFECTS parameter can be used to supply effects, for plotting in the x-axis margin. The population type must then also be specified by the
POPULATIONTYPE option, The plot contains 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 lines of squares, according to the length of the
QSE pointers. 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. The brightness of the colour of each square indicates the significance of its effect. The
KEYWINDOW option specifies the number of a window to contain a key for the plots; default 2. The
IDPARENTS parameter can supply labels for the parents, to appear in the key. You can set
KEYWINDOW=0 to suppress the key.
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 sumbols (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 be used to provide a title for the graph. By default, the plot is sent to the screen. However, you can supply a file for the plot, using the
DFILENAMEparameter. You can discover the types of graphics file that are supported by running the command
XTITLE options can supply titles for the y- and x-axis, respectively. If
YTITLE is not specified, a default title is used, showing the identifier of the
STATISTICS variate. The upper bound of the y-axis can be set by the
YUPPER option. The
WINDOW option specifies the window in which the graph is drawn (default 1), and the
SCREEN parameter controls whether the screen is cleared before the graph is displayed..
Restrictions are not allowed.
CAPTION 'DQSQTLSCAN example'; STYLE=meta SPLOAD [PRINT=*] '%GENDIR%/Examples/F2maizemarkers.GWB'; SHEET='LOCI' SPLOAD [PRINT=*] '%GENDIR%/Examples/F2maize_single_out.gwb' SCALAR thres; VALUE=3.21 "from QSQTLSCAN" DQSQTLSCAN [POPULATIONTYPE=F2; METHOD=line; THRESHOLD=thres;\ TITLE='Yield'; YUPPER=10]\ CHROMOSOMES=mkchr; POSITIONS=mkpos; STATISTICS=minlog10p;\ QEFFECTS=qeff2; QSE=qse2 DQSQTLSCAN [POPULATIONTYPE=F2; METHOD=spikes; THRESHOLD=thres;\ TITLE='Yield'; YUPPER=10]\ CHROMOSOMES=mkchr; POSITIONS=mkpos; STATISTICS=minlog10p;\ QEFFECTS=qeff2; QSE=qse2; IDEFFECTS=!t(additive,dominance);\ IDPARENTS=!t(Parent1,Parent2) DQSQTLSCAN [METHOD=line; THRESHOLD=thres; TITLE='Yield']\ CHROMOSOMES=mkchr; POSITIONS=mkpos; STATISTICS=minlog10p DQSQTLSCAN [POPULATIONTYPE=F2; DCHROMOSOMES=9; METHOD=line;\ THRESHOLD=thres; TITLE='Yield'] \ CHROMOSOMES=mkchr; POSITIONS=mkpos; STATISTICS=minlog10p;\ QEFFECTS=qeff2; QSE=qse2 DQSQTLSCAN [DCHROMOSOMES=9; METHOD=spikes; THRESHOLD=thres; TITLE='Yield']\ CHROMOSOMES=mkchr; POSITIONS=mkpos; STATISTICS=minlog10p DQSQTLSCAN [POPULATIONTYPE=F2; DCHROMOSOMES=!(1,9); METHOD=spikes;\ THRESHOLD=thres; TITLE='Yield']\ CHROMOSOMES=mkchr; POSITIONS=mkpos;\ STATISTICS=minlog10p; QEFFECTS=qeff2; QSE=qse2;\ IDEFFECTS=!t(additive,dominance); IDPARENTS=!t(Parent1,Parent2)