[Solved] Highlight specific genes in boxplot

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I’ll give you a ggplot2 answer. For this, you need to reshape your data, so there are separate x and y variables. Right now, your y values are split between two columns.

Then we highlight the specific genes by only plotting points for a subset.

library(ggplot2)
library(dplyr)
library(tidyr)

gene_list <- c('C', 'F', 'G', 'I')
df_long <- gather(df, treatment, expression, -Gene)

ggplot(df_long, aes(treatment, expression)) +
  geom_boxplot() +
  geom_point(aes(color = Gene), filter(df_long, Gene %in% gene_list), size = 3) + 
  theme_minimal() +
  labs(caption = 'p < 0.001')

enter image description here

For specific adjustments, please have a look at the many ggplot2 questions here on SO.

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solved Highlight specific genes in boxplot