How to extend the x axis in Dimplot Seurat

Question

I have performed a Seurat PCA via Dimplot.

How do I extend the x axis?

As you can see in my figure the double x axes overlap.

Answer 1

Looking at the source code for Seurat's DimPlot() it's based on ggplot2 graphics (https://github.com/satijalab/seurat/blob/HEAD/R/visualization.R#L794), so you can manipulate the dimplot object and save it using ggplot2 commands. Using ggsave() you can specify the figure dimensions; if you increase the width of the final figure it should 'fix' your label overlap issue, i.e.

#BiocManager::install("Seurat")
library(Seurat)
#> Attaching SeuratObject
library(ggplot2) # for plotting
library(cowplot) # for the theme used by Seurat

# example data
data("pbmc_small")
p <- DimPlot(object = pbmc_small, split.by = "ident")

# example dimplot
p

# increase font size to make the labels overlap
p +
  theme_cowplot(font_size = 28) +
  theme(strip.background = element_blank())

# save the 'overlapping label' figure and specify a relatively large width to 'space out' the three facets
ggsave("dimplot_test.png", width = 40, height = 10, units = "cm")

---

You could also decrease the font size and keep the original dimensions to fix the problem, or alter the breaks on the x axis, e.g.

# reduce the size of the x axis text labels
p +
  theme_cowplot() +
  theme(strip.background = element_blank(),
        axis.text.x = element_text(size = 8))

# change the number of breaks
p +
  theme_cowplot() +
  theme(strip.background = element_blank()) +
  scale_x_continuous(breaks = scales::pretty_breaks(n = 2))

# Specify the breaks you want to use
p +
  theme_cowplot() +
  theme(strip.background = element_blank()) +
  scale_x_continuous(breaks = c(-20, 0, 20, 40))

^{Created on 2022-12-01 with reprex v2.0.2}

Answer 2

As a direct answer to your question, restrict the output to producing a single column:

Dimplot(..., ncol=1)

But this doesn't seem like a useful answer. Please provide more context to your question if you want more help than this.