Question: plotting two genes in Seurat ScRNAseq
0
gravatar for rob.costa1234
2.3 years ago by
rob.costa1234250
United States
rob.costa1234250 wrote:

I have a clarification about about using Seurat package (link is https://satijalab.org/seurat/pbmc3k_tutorial.html)-

FeaturePlot(object = pbmc, features.plot = c("MS4A1", "GNLY", "CD3E", "CD14", 
    "FCER1A", "FCGR3A", "LYZ", "PPBP", "CD8A"), cols.use = c("grey", "blue"), 
    reduction.use = "tsne")

At this time only one gene is plotted on the cluster. Can I plot two genes simultaneously in different colors on the clusters? if so how can I do that.

Thanks

rna-seq • 5.2k views
ADD COMMENTlink modified 2.2 years ago by dppb0590 • written 2.3 years ago by rob.costa1234250

Can I plot two genes simultaneously in different colors on the clusters?

Let me see if I understood correctly: you wish to plot the expression of several genes, each with a different colour, in a single tSNE plot?

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by dppb0590

Yes that is exactly what I want to do

ADD REPLYlink written 2.2 years ago by rob.costa1234250
1
gravatar for dppb05
2.2 years ago by
dppb0590
dppb0590 wrote:

Can I plot two genes simultaneously in different colors on the clusters?

If it is just two genes, the overlay option in Seurat's FeaturePlot can help you with that.

FeaturePlot(object = pbmc,
    features.plot = c("LYZ", "CD8A"),
    cols.use = c("grey", "blue", "red", "pink"), 
    reduction.use = "tsne",
    overlay = TRUE)

The cols.use parameter indicate, respectively, low expression of both genes, high expression of LYZ, high epxression of CD8A, and high expression of both genes. Of course, you can change the colours and genes as you prefer, but keep in mind that you can only use two genes and four colours. If you pass less than four colours the other colours are going to be defined automatically by Seurat.

ADD COMMENTlink written 2.2 years ago by dppb0590

Sorry, how I can change the color of some cells in feature plot? I have a list of cells, I would like to map them in feature plot

ADD REPLYlink written 2.2 years ago by Za130

@Za There are a few different ways you can do that. I suggest you create a new post with your question detailing a bit how your list of cells is stored.

ADD REPLYlink written 2.2 years ago by dppb0590

Hi! Za i wanna know do you figure how to plot several genes simultaneously in Featureplot? because i am also find how to do with it.

ADD REPLYlink written 23 months ago by biologo40

For mapping several cells this is the solution

https://bioinformatics.stackexchange.com/questions/4470/mapping-a-list-of-cells-in-seurat-featureplot

for mapping several genes if I am not wring by a vector of those genes you can do that by seurat

FeaturePlot(object = seurat,features.plot = c("list of your genes"))
ADD REPLYlink modified 23 months ago • written 23 months ago by Za130
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