4.3 MQTLView

MQTLView is designed to depict the result of the QTL clustering for one or several chromosomes on a given map.

4.3.1 Command Line Options

Option	Usage	Type	Explanation
-m,--map	required	string	The XML file for the genetic map.
-c,--chrom	required	string	The name of the chromosome (or a list separated by comma) to display.
-o,--output	required	string	The output file stem.
-r,--clust	optional	string	The file of the clustering result.
-b,--best	optional	string	The file of the best clustering (only with -c).
-t,--tree	optional	string	The file of the hierarchical clustering result.
--mode	optional	integer	The mode of representation (0 or 1 and only with -c and -b)
--trait	optional	string	The name of the trait.
-p,--parfile	optional	string	The drawing parameter file.
--img	optional	string	The format of the image (use –help for possible values).

MQTLView provides several ways to represent the results of the QTL clustering depending on the algorithm used to perform it. Suppose we have first done a clustering using QTLClust See QTLClust, which produced the result file clust_res.txt. From the output file clust_model.txt generated by QTLClust we have derived the file clust_best.txt which gives for a given trait the best clustering model for each chromosome (according to a given model choice criterion):

Chromosome Trait Model 3 FT 5 10 FT 4 5 FT 4 7 FT 5 2 FT 4 9 FT 2 4 FT 3 8 FT 5 6 FT 3 1 FT 2

Then, we can run MQTLView to visualize the result, for example on chromosome 8 and 9 together, by invoking the command

%java org.metaqtl.main.MQTLView \ > -c 8,9 -m map.xml -r clust_res.txt -b clust_best.txt -o figure --img jpeg

By default the figure is created with the mode --mode 1 which leads to something like that

Now, if you set the option --mode to `0', i.e

%java org.metaqtl.main.MQTLView \ > -c 8,9 -m map.xml -r clust_res.txt -b clust_best.txt -o figure --img jpeg --mode 0

you will obtain the following representation

where the first bar which follows the name of the QTL corresponds to the relative CI of the QTL (i.e. that the more the bar is filled, the larger the CI is). The second bar gives the membership probabilities of the QTL according to the meta-QTL model.

If the clustering have been done via QTLTree, the result file obtained tree.txt can be passed to MQTLView as follows,

%java org.metaqtl.main.MQTLView \ > -c 3 -m map.xml -t tree.txt -o figure --img jpeg

In this case MQTLView draws the tree obtained by the hierarchical clustering procedure as illustrated in the next figure.

Finally the results from QTLClust and QTLTree can be visualized together as shown bellow.

%java org.metaqtl.main.MQTLView \ > -c 3 -m map.xml -r clust_res.txt -b clust_best.txt -t tree.txt -o figure --img jpeg