Add small arrows instead of axis to UMAP-CodePudding

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?

CodePudding user response：

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
)

CodePudding user response：

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)