Hi thomasd,
It sounds like you're running a hierarchical cluster analysis, is that right? For that analysis output the rows are rearranged to form the dendrogram, so we'll need to do something else to form the graphic I think you want. If you're looking to preserve your row ordering and show lipidomic concentration in a heat map, perhaps Graph > Cell Plot will work for you.
Here's a simple example with the Big Class sample data set:
And here is a bigger example using the Blood Pressure sample dataset, with 4 levels of the experimental factor, and 6 DVs:
Does that get close to what you're looking for? If not, can you provide an image of the kind of plot you're looking to make? I'm sure we can find a way to make it with JMP.
Hope this helps!
julian