Is it possible to identify cells that are expressing two or more genes in Seurat?
The counts stored in the Seurat object are: raw counts (seuratobject@raw.data), the log + normalized counts (seuratobject@data), and the scaled counts (seuratobject@scale.data). FeaturePlot() plots the log + normalized counts.

In order to identify double-positive cells, you need to identify cells that express a gene (i.e. positive for a gene) and that is not trivial: you need a cutoff value for each gene, and also to distinguish between true and dropout zero counts.

Provided you solve these, you can retrieve your cells by:

MYH11.cutoff &lt;- 1
ACTA2.cutoff &lt;- 1
length(which(FetchData(seuratobject, vars.all='MYH11') &gt; MYH11.cutoff))
length(which(FetchData(seuratobject, vars.all='ACTA2') &gt; ACTA2.cutoff))
length(which(FetchData(seuratobject, vars.all='MYH11') &gt; MYH11.cutoff &amp; FetchData(seuratobject, vars.all='ACTA2') &gt; ACTA2.cutoff))