How do I prevent the FeatureHeatmap function from the Seurat package, from sorting my data groups in alphabetical order when plotting data?
I had this same issue. I reordered the levels and that worked for most functions, but would switch back with the FeatureHeatmap. Turns out there is a line in the function that changes it to a character. 

I ended up making a "new" function and just changed that one line from:

data.plot$ident &lt;- as.character(x = object@ident)


to:

data.plot$ident &lt;- object@ident


Once that was fixed, the order that I assigned worked out just fine.