4.1 MapView

MapView is designed to draw markers and QTL for one or several linkage groups, depending on drawing parameters.

4.1.1 Command Line Options

Option	Usage	Type	Explanation
-m,--mapfile	required	string	The XML file for the genetic map.
-c,--chrom	required	string	The name of the chromosome(s) to display.
-o,--output	required	string	The output file stem.
-q,--withqtl	optional	integer	Draw also QTL.
-t,--tonto	optional	string	The XML file for the trait ontology
-p,--parfile	optional	string	The drawing parameter file.
--qmode	optional	integer	QTL representation mode (0=bar,1=arrow)
--tree	optional	string	a QTL tree (obtained with QTLTree);
--img	optional	string	The format of the image (use –help for possible values).

For example,

%java org.metaqtl.main.MapView \ > -c 1,2 -m map.xml -q -o figure --img jpeg

draws the chromosome 1 and 2 with both markers and QTL of the given map map.xml and outputs the result in figure.jpeg. This also creates a file named figure.par which gives the values of the drawing paremeters. This file can be modified and reused to create another image by using the -p or --par option

%java org.metatqtl.main.MapView \ > -c 1,2 -m map.xml -q -o figure -p figure.par --img jpeg

The next section gives more details on how to deal with the drawing parameters.

4.1.2 Drawing Parameters

Several parameters allow user to put in form the figure. The next figure illustrates the role of each parameter.

Figure 4.1: Details of formatting parameters for MapView.

# # Graphical Parameters # # CHROMOSOME # CHROM_DISTANCE_SCALE=5.0 CHROM_FLANKING_CEX=0.1 CHROM_NAME_FONT=Utopia Regular:BOLD:12 CHROM_NAME_HSPACE=20.0 CHROM_TICK_WIDTH_1=10.0 CHROM_TICK_WIDTH_2=20.0 CHROM_TICK_WIDTH_3=10.0 CHROM_WIDTH=30.0 MAKER_NAME_VSPACE=1.0 MARKER_NAME_FONT=Utopia Regular:PLAIN:10 MARKER_POSITION_FONT=Utopia Regular:PLAIN:10 # # QTL # QTL_CI_WIDTH=10.0 QTL_CI_WIDTH_CEX=0.25 QTL_HSPACE=10.0 QTL_NAME_FONT=Courier:PLAIN:10 QTL_NAME_VSPACE_CEX=1.0 QTL_POS_HEIGHT_CEX=0.01 QTL_POS_WIDTH_CEX=1.5 QTL_VSPACE=20.0 # # LEGEND # LEGEND_BOX_CEX=0.5 LEGEND_FONT=Verdana:PLAIN:10 LEGEND_HSPACE=5.0 LEGEND_PART_HEIGHT=20.0 LEGEND_PART_WIDTH=50.0 LEGEND_SCALE_UNIT=5 # # OTHER # BACKGROUND_COLOR=ffffff LAYER_HSPACE=20.0 LAYER_VSPACE=20.0 WITH_CHROM_NAME=true WITH_LEGEND=true WITH_MAP_NAME=true WITH_MARKER_NAME=true WITH_QTL_NAME=true WITH_MARKER_POSITION=true

A line which begins by the character `#' is ignored by the program. Each drawing parameter is specified by its own name directly followed by a sign `=' and its value. For the parameters which specify a color (those which end by `_COLOR') the value must be a RGB code in hexadecimal (e.g red is ff0000, green 00ff00, blue 0000ff, white ffffff, black 000000, and etc...). For the parameters which specify a font (those which end by `_FONT') the value must be a string composed by 3 tokens separated by a `:'. The first token gives the name of the font, the second one the style of the font (among `PLAIN,BOLD' and `ITALIC') and the last one indicates the size of the font. The parameter file generated by MapView ends by a list of the available fonts on your system. If you do not use a font name in this list, then MapView will use the default font. The parameters which start by `WITH_' allow the user to specify if the corresponding elements of the figure must be drawn. The possible values for these parameters are either `true' (draw) and `false' (not to draw). For example if you set `WITH_MARKER_POSITION=false' the marker positions along the chromosome wont' be drawn. When the QTL are added to the figure (option -q with MapView) they are colored according to their trait group. The colors used to display the QTL are also specified in the parameter file generated by the program. For example, let's assume that the QTL belongs to 3 trait groups. The parameter file will then contain the following lines:

# # COLOR PALETTE # QTL_COLOR_1=ffff00 QTL_COLOR_2=00ff00 QTL_COLOR_3=0000ff

where QTL_COLOR_i is the color of the group i. You can use these lines to modify the default colors.