Question: plotting two genes in Seurat ScRNAseq
0
gravatar for rob.costa1234
11 months ago by
rob.costa1234160
United States
rob.costa1234160 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 • 2.2k views
ADD COMMENTlink modified 11 months ago by dppb0570 • written 11 months ago by rob.costa1234160

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 11 months ago • written 11 months ago by dppb0570

Yes that is exactly what I want to do

ADD REPLYlink written 11 months ago by rob.costa1234160
1
gravatar for dppb05
11 months ago by
dppb0570
dppb0570 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 11 months ago by dppb0570

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 10 months ago by Za120

@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 10 months ago by dppb0570

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 7 months ago by biologo20

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 7 months ago • written 7 months ago by Za120
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