Hi,
I have 209 cells, I have clustered them by Seurat to 4 clusters. By Featureplot
> FeaturePlot(object = seuset_16,
+ features.plot = "DDB_G0273311")
+ )
>
I am able to track this gene in clusters like this picture:
Higher color shows higher expression and vice versa, however I don't know the threshold, so I don't know when two different genes become yellow which of them really express more.
So, 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
https://drive.google.com/file/d/1rLsRXrxJPYm8cSzSqa5WUR6NYaUr-e9f/view?usp=sharing.
Featureplot or whatever are in this object but unfortunately I am not able to manipulate them
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 https://drive.google.com/file/d/1sks1fwe2yWCQp8n7WFUB480pnECBdhPk/view?usp=sharing
I have coloured cells that express a gene > mean + se, < 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?