Mapping a list of cells in seurat featureplot I have 209 cells, I clustered them by Seurat to 4 clusters. By Featureplot I am able to track a gene in clusters:


Higher color shows higher expression. 

Now, for some genes I want to highlight some cells in Featureplot so that apart from yellow or red colours I want to colour a subsets of cells with another color. I mean I want to map a list of cells in Featureplot or tSNE plot. Let's say I want to know the location of cells 1, 4, 80 and highlight them with another color. 
My Seurat object in this link.

Seurat itself beautifully maps the cells in Featureplot for defined genes with a gradient of colours showing the level of expression. Saying I have genes A and B, in excel.

I have coloured cells that express a gene > mean + se, &lt; mean - se or between these values. For instance, for this gene, 36 cells express this gene > mean + se, I want to map these cells in Featureplot or tSNE plot in distinct colour so I can locate them in clusters easily. Something like binary (on off) expression to relative expression.

How I can change the colour of some cells based on my threshold for this gene please?
To color the TSNEPlot, you can generate a new column in metadata with the expression levels (High, low, etc). Then use pt.shape to set a shape for each identity.

To show binary expression based on expression you first have to define the list of cells that are below or over your threshold. Once you have those lists you can use SetIdent() in Seurat to color those groups. 

load(file= "~/seuset_16.RData")

high &lt;- c("s1.1","s1.4", "s1.80")  
low &lt;- setdiff(colnames(seuset_h16@data), high)  
seuset_h16 &lt;- SetIdent(seuset_h16, cells.use = high, ident.use = "high")  
seuset_h16 &lt;- SetIdent(seuset_h16, cells.use = low, ident.use = "low") 
seuset_h16 &lt;- StashIdent(seuset_h16, save.name = "expr")  
seuset_h16 &lt;- SetAllIdent(seuset_h16, id="res.1")  
t &lt;- TSNEPlot(seuset_h16, pt.size = 2, do.return = T, pt.shape ="expr")  
t




high &lt;- c("s1.1","s1.4", "s1.80")  
low &lt;- setdiff(colnames(seuset_h16@data), high)  
seuset_h16 &lt;- SetIdent(seuset_h16, cells.use = high, ident.use = "high")  
seuset_h16 &lt;- SetIdent(seuset_h16, cells.use = low, ident.use = "low")   
t &lt;- TSNEPlot(seuset_h16, pt.size = 2, do.return = T, colors.use = c("red", "grey"), do.hover =T, data.hover =c("ident", "res.1))  
t