Without example code we can't reproduce your problem, but yes you can definitely customize axis tick labels.
For example, after generating your plot p with ggplot2, you can customize tick labels using
p + scale_x_discrete(labels=c("original_label1" = "new_label1", "original_label2" = "new_label2",
"original_label3" = "new_label3"))
This way you are manually customizing tick labels.