Add small arrows instead of axis to UMAP

Question

More often I see in publications that instead of printing the UMAP axis in scRNAseq experiments (or even t-SNE or PCA) they just add two small arrows in the bottom left corner. Something like this:

I really like the aesthetics of it but I don´t know how to replicate this in R. I guess this is normally done separately with some image editor but it can probably be done with ggplot2 package to make it more reproducible. So far I only got the arrows in the axis:

x <- data.frame(UMAP1=rnorm(300),UMAP2=rnorm(300))
ggplot(x, aes(UMAP1,UMAP2)) + geom_point() + theme_minimal() +
theme(axis.line = element_line(arrow = arrow(type='closed', 
      length = unit(10,'pt'))))

But I don't know how to make them smaller and with the title underneath. Does anyone have any suggestions on how to do this?

It's easier to help you if you include a simple [reproducible example](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) with sample input that can be used to test and verify possible solutions. — MrFlick, Dec 07 '22 at 17:35

score 1 · Answer 1 · answered Dec 07 '22 at 18:08

I'd suggest faking it with an annotation:

library(dplyr); library(umap); library(ggplot2)
arr <- list(x = -10, y = -15, x_len = 5, y_len = 5)
ggplot(storms_umap_extract, aes(x,y, color = category, alpha = wind)) +
  geom_point() +
  annotate("segment", 
           x = arr$x, xend = arr$x + c(arr$x_len, 0), 
           y = arr$y, yend = arr$y + c(0, arr$y_len), 
           arrow = arrow(type = "closed", length = unit(10, 'pt'))) +
  theme_void()

Here's the umap data:

storms_umap <- storms |>
  select(lat,long, wind, pressure) |>
  umap() # this took about a minute to run

storms_umap_extract <- tibble(
  x = storms_umap$layout[,1],
  y = storms_umap$layout[,2],
  wind = storms_umap$data[,3],
  category = storms$category
)

score 1 · Accepted Answer · answered Dec 07 '22 at 18:40

In code below, adjust unit(3, "cm") and hjust = 0 to taste. Disclaimer: I wrote ggh4x.

library(ggplot2)

axis <- ggh4x::guide_axis_truncated(
  trunc_lower = unit(0, "npc"),
  trunc_upper = unit(3, "cm")
)

x <- data.frame(UMAP1=rnorm(300),UMAP2=rnorm(300))

ggplot(x, aes(UMAP1, UMAP2)) +
  geom_point() +
  guides(x = axis, y = axis) +
  theme(axis.line = element_line(arrow = arrow()),
        axis.title = element_text(hjust = 0))

^{Created on 2022-12-07 by the reprex package (v2.0.1)}

Optionally, add the code below if you want to get rid of the ticks and labels (which don't make any sense in terms of UMAP/tSNE anyway)

scale_x_continuous(breaks = NULL) +
scale_y_continuous(breaks = NULL)

Add small arrows instead of axis to UMAP

2 Answers2