Plots the results of a genome-wide scan for QTL effects in multi-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 |
|---|---|
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 colours of pens 1, 2 up to the number of chromosomes |
TITLE = text |
General title |
YLOWERTITLE = text |
Title for the y-axis of the lower graph; default 'Environments' |
YUPPERTITLE = text |
Title for the y-axis of the upper graph; default uses the identifier of the STATISTICS variate or pointer |
XTITLE = text |
Title for the x-axis; default 'Chromosomes' |
YAXUPPER = scalar |
Upper bound for y-axis of the upper graph |
ANNOTATION = string token |
Whether to include annotation of the effects in the plot (include, omit); default incl |
Parameters
STATISTICS = variates or pointers |
Test statistics to be plotted; must be set |
|---|---|
CHROMOSOMES = factors |
Chromosome for each locus; must be set |
POSITIONS = variates |
Positions on the chromosome of each locus; must be set |
QEFFECTS = pointers |
QTL effects in the different environments; must be set |
QSE = pointers |
Standard errors of the QTL effects in the different environments; must be set |
ENVNAMES = texts |
Labels for the different environments; must be set |
IDEFFECTS = texts |
Labels to use to identify the effects |
IDPARENTS = texts |
Labels to use to identify the parents |
DFILENAME = texts |
Name of the graphics file for the plots |
Description
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 CHROMOSOMES and 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 THRESHOLD scalar.
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 QEFFECTS and QSE pointers. Titles for the plots can be supplied by the IDEFFECTS parameter. 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. 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.
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 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.
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 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 'environments'. The 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 YAXUPPER option.
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 DHELP possible.
Options: POPULATIONTYPE, METHOD, THRESHOLD, DCHROMOSOMES, SUPPRESSLINES, SYMBOL, SIZEMULTIPLIER, BLACKOUTLINE, COLOURS, TITLE, YLOWERTITLE, YUPPERTITLE, XTITLE, YAXUPPER, ANNOTATION.
Parameters: STATISTICS, CHROMOSOMES, POSITIONS, QEFFECTS, QSE, ENVNAMES, IDEFFECTS, IDPARENTS, DFILENAME.
Action with RESTRICT
Restrictions are not allowed.
See also
Procedures: DQMAP, DQMKSCORES, DQSQTLSCAN, QMKDIAGNOSTICS.
Commands for: Statistical genetics and QTL estimation, Graphics.
Example
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)