Seurat Merged objects tSNE - How to paint on original IDs?
Below a few lines of code that accompany BC Wang's answer.
After using MergeSeurat the sample name will be added to meta data under orig.ident. this can then be used to color the tSNE either using group.by or pt.shape. The former will show colors for each sample, the latter will color each cluster and give sample id another shape.

path1 &lt;- file.path("path to 10x sample 1")
path2 &lt;- file.path("path to 10x sample 2")

S1 &lt;- Read10X(data.dir = path1)
S2 &lt;- Read10X(data.dir = path2)
S1 &lt;- CreateSeuratObject(raw.data = S1, min.cells = 3, project = "S1")
S2 &lt;- CreateSeuratObject(raw.data = S2, min.cells = 3, project = "S2")

s.combined &lt;- MergeSeurat(object1 = S1, object2 = S2, add.cell.id1 = "S1", 
            add.cell.id2 = "S2", project = "2samples")


All data analysis goes here:
RunTSNE etc...

Plot the data

TSNEPlot(s.combined, group.by ="orig.ident")
TSNEPlot(s.combined, pt.shape="orig.ident")