Plots the results of a genome-wide scan for QTL effects in single-environment trials (M.P. Boer & J.T.N.M. Thissen).
Options
POPULATIONTYPE = string token |
Type of population (BC1, DH1, F2, RIL, BCxSy, CP); must be set when QEFFECTS are supplied |
|---|---|
METHOD = string token |
Method to be used for plotting (line, manhattan, spikes); default line |
THRESHOLD = scalar |
Threshold value for test statistic; default 0 |
DCHROMOSOMES = scalar, text or variate |
Allows a subset chromosomes to be specified to display; default * i.e. all the chromosomes |
SUPPRESSLINES = string token |
Whether to suppress the vertical lines between the chromosomes (yes, no); default no |
SYMBOL = scalar |
Defines the plotting symbol for each point, as in the SYMBOL option of PEN, when METHOD=manhattan; default 2 i.e. circle |
SIZEMULTIPLIER = scalar |
Multiplier used in the calculation of sizes of symbols when METHOD=manhattan; default 1 |
BLACKOUTLINE = string token |
Whether to draw the outer line the SYMBOL in black when METHOD=manhattan (yes, no); default no |
COLOURS = scalar, variate or text |
Colours to use for the chromosomes; default * uses the default colours of pens 1, 2 up to the number of chromosomes |
TITLE = text |
General title |
YTITLE = text |
Title for the y-axis; default uses the identifier of the STATISTICS variate or pointer |
XTITLE = text |
Title for the x-axis; default 'Chromosomes' |
YUPPER = scalar |
Upper bound for y-axis |
WINDOW = scalar |
Window number for the graphs; default 1 |
KEYWINDOW = scalar |
Window number for key (zero for none); default 2 |
SCREEN = string token |
Whether to clear the screen before displaying the graph (clear, keep); default clea |
Parameters
STATISTICS = variates or pointers |
Test statistic(s) to be plotted; must be set |
|---|---|
CHROMOSOMES = factors |
Chromosome for each locus; must be set |
POSITIONS = variates |
Position on the chromosome for each locus; must be set |
QEFFECTS = variates or pointers |
QTL effects along the genome, |
QSE = variates or pointers |
Standard errors of the QTL effects |
IDEFFECTS = texts |
Labels along the x-axis to identify the effects when QEFFECTS are supplied |
IDPARENTS = texts |
Labels to use to identify the parents |
DFILENAME = texts |
Name of the graphics file for the plots |
Description
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.
The 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 QEFFECTS and QSE pointers. The first element of the QEFFECTS and 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.
If the 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 SYMBOL, SIZEMULTIPLIER and 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.
The 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.
The 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 DHELP possible.
The YTITLE and 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..
Options: POPULATIONTYPE, METHOD, THRESHOLD, DCHROMOSOMES, SUPPRESSLINES, SYMBOL, SIZEMULTIPLIER, BLACKOUTLINE, COLOURS, TITLE, YTITLE, XTITLE, YUPPER, WINDOW, KEYWINDOW, SCREEN.
Parameters: STATISTICS, CHROMOSOMES, POSITIONS, QEFFECTS, QSE, IDEFFECTS, IDPARENTS, DFILENAME.
Action with RESTRICT
Restrictions are not allowed.
See also
Procedures: DQMAP, DQMKSCORES, DQMQTLSCAN, QMKDIAGNOSTICS.
Commands for: Statistical genetics and QTL estimation, Graphics.
Example
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)