ViolinPlot x-axis

Question

I'm trying to set the x-axis in my Violin Plot to go by each patient rather than it being scattered.

VlnPlot(obj, features = c("classical_basal"), pt.size = 0) + NoLegend() + theme(axis.text.x = element_text(angle = 90, hjust = 1))

The above code gives me the x-axis but there is no pattern or order. I would like the x-axis to be grouped with the HTB, for example ALL of the HTB2867 first, followed by HTB2876, etc...

Answer 1

Seurat does violin plots using ggplot, which orders based on the factor levels. You need to re-factor your grouping category so that the levels matches your preferred order:

# default level sort order is alphabetical
obj[["grouping"]] <- factor(unlist(obj[["grouping"]])) # refactor
VlnPlot(obj, group.by = "grouping", features = c("classical_basal"),
        pt.size = 0) +
  NoLegend() + theme(axis.text.x = element_text(angle = 90, hjust = 1))

Answer 2

It is difficult to say exactly what you would like to achieve without an example.

But if you would like an individual axis based on a factor like patient maybe you want to use facet_wrap for the Patient variable like in the example below?

library(ggplot2)

data <- iris

ggplot(data, aes(x=Sepal.Width, y=Sepal.Length, fill=Species)) +
  geom_violin() +
  facet_wrap(~Species, scales="free_x")
```