The
Estimate Plots
tab is shown below:
The V
olcano Plots
tab contains the following elements:
|
•
|
A
Volcano Plot
for each quantitative trait.
|
The
volcano plot
(s) show the
LOD score
for each
trait
plotted on the
y
-axis versus either the
Estimate of the Additive Effect
on the
x
-axis or the
Estimate of the Dominance Effect
(coded in reference to the effect of the parental line 2 or P2
allele
). Each point on the plot represents a
QTL
testing location, with points colored by the
chromosome
or
linkage
group. Negative estimates indicate that there was a decrease in the quantitative trait associated with the allele from parental line 2. The black horizontal line represents a LOD threshold that was either specified on the process
dialog
or determined using permutation testing. Points to the upper left or upper right indicate locations with increasing evidence of a significant QTL that have large negative or positive effect on the trait of interest.
The JMP
Data Filter
has also been embedded into this tabbed view to use for interactively selecting points in the plots.