Highlight all values from single column

You were right about scalecolormanual, the code below uses it.

Color by name and then change the colors to the colors you want, in this case, gene1 is red and all others black.
The colors vector clrs is created based on the original data.frame, so if there are more genes the code below should still work.

suppressPackageStartupMessages({
  library(ggplot2)
  library(dplyr)
  library(tidyr)
})
create a colors named vector
genes  1     A   0.5 -0.40  0.02
#> 2     B   1.0  0.05 -0.30
#> 3     C  -0.8  0.10  0.15

^{Created on 2026-01-28 with reprex v2.1.1}

library(ggplot2)
library(gghighlight)
df |> 
  tidyr::pivotlonger(!Indiv) |>
  ggplot(aes(x = Indiv, y = value)) + 
  geompoint(aes(group=name, color = name), size = 2) +
  gghighlight(name == "gene1", 
              usedirectlabel = FALSE, usegroupby = FALSE, 
              unhighlightedparams = list(color = "black")) +
  themebw() +
  theme(legend.title = element_blank())

^{Created on 2026-01-28 with reprex v2.1.1}

Here's one way to highlight just one gene. Create a function that accepts your data and the gene number that you want to highlight:

plot_gene