Getting coordinates for the label locations from ggrepel, Cytoscape, https://stackoverflow.com/questions/45065567/getting-coordinates-for-the-label-locations-from-ggrepel, tested and works under R 4.1.1

repelling_labels.r

x = c(0.8846, 1.1554, 0.9317, 0.9703, 0.9053, 0.9454, 1.0146, 0.9012, 0.9055, 1.3307)
y = c(0.9828, 1.0329, 0.931, 1.3794, 0.9273, 0.9605, 1.0259, 0.9542, 0.9717, 0.9357)
ShortSci = c("MotAlb", "PruMod", "EriRub", "LusMeg", "PhoOch", "PhoPho", 
         "SaxRub", "TurMer", "TurPil", "TurPhi")
df <- data.frame(x = x, y = y, z = ShortSci)
 
library(ggplot2)
library(ggrepel)
p1 <- ggplot(data = df, aes(x = x, y = y)) + theme_bw() + 
  geom_text_repel(aes(label = z), 
                  box.padding = unit(0.45, "lines")) +
  geom_point(colour = "green", size = 3)
x11(width=7,height=7)
p1
 
# Get x and y plot ranges 
ggp1 <- ggplot_build(p1)
xrg <- ggp1$layout$panel_params[[1]]$x.range
yrg <- ggp1$layout$panel_params[[1]]$y.range
 
library(grid)
grid.force()
kids <- childNames(grid.get("textrepeltree", grep = TRUE))
 
# Function: get the x and y positions of a single ggrepel label
get.xy.pos.labs <- function(n) {
  grb <- grid.get(n)
  data.frame(
  x = xrg[1]+diff(xrg)*convertX(grb$x, "native", valueOnly = TRUE),
  y = yrg[1]+diff(yrg)*convertY(grb$y, "native", valueOnly = TRUE)
  )
}
 
 
# Get positions of all ggrepel labels
dts <- do.call(rbind, lapply(kids, get.xy.pos.labs))
dts$lab <- df$z
print(dts)
 
# Plot labels using the positions calculated using get.xy.pos.labs      
p2 <- ggplot(data = df, aes(x = x, y = y)) + theme_bw() + 
  geom_text(aes(x=x,y=y, label=lab), data=dts, col="red", inherit.aes=F)+
  geom_point(colour = "green", size = 3) 
 
x11(width=7,height=7)
p2