Question: In Seurat, what data is VlnPlot() plotting?
0
gravatar for Kristin Muench
7 months ago by
United States
Kristin Muench450 wrote:

Hello,

I'm using the Seurat function VlnPlot() to visualize some of my data.

VlnPlot(object = data.combined, features.plot = c( 'Xist' )

When I plot it, the values range between 0 and 5.

I then wanted to extract the expression value matrix used to generate VlnPlot. By peeking inside the VlnPlot command, it looks like this is the command used to extract data:

exprs <- data.frame(FetchData(object = data.combined, vars.all = c('Xist' ) ), check.names = F)

However, when I run that, the values range between 0 and 120 - that is, they seem unscaled.

I see those same values no matter what I'm pulling for FetchData:

exprs <- data.frame(FetchData(object = data.combined, vars.all = c('Xist' ) ), use.imputed = T)
exprs <- data.frame(FetchData(object = data.combined, vars.all = c('Xist' ) ), use.scaled = T)
exprs <- data.frame(FetchData(object = data.combined, vars.all = c('Xist' ) ), use.raw = T)

What is VlnPlot doing differently to get data that only ranges between 0 through 5?

Thank you for your help.

ADD COMMENTlink modified 7 months ago • written 7 months ago by Kristin Muench450
1
gravatar for Kristin Muench
7 months ago by
United States
Kristin Muench450 wrote:

UPDATE: It looks like the issue lied in confusing a combined Seurat object representing multiple samples and using an object that had a single sample. Previously, I had been plotting VlnPlot on combined sample, but accidentally trying to extract data from a single sample, which I'm guessing had not been scaled/regressed correctly, thus causing the confusion. Once I corrected this bug, this works as I would expect now:

exprs <- data.frame(FetchData(object = data.combined, vars.all = c('Xist' ))
ADD COMMENTlink written 7 months ago by Kristin Muench450
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1335 users visited in the last hour