How to remove percentage breakdowns from a legend created by ggplot2

Krutik Published at Dev

Krutik

I have made a plot displaying multiple facets of my data. The colour bar created by scale_colour_gradientn is confusing because it shows percentage breakdowns. Could I get rid of these percentage breakdowns and add my own. I have tried using values and breaks parameters but with no luck. I think maybe ggplot is confused because most of the values are either very small or close to 1. I have added a toy dataset, code and image output below.

dput(df)

structure(list(Mean.Count = c(30404.8407153174, 15689.4221807262, 
30404.8407153174, 15689.4221807262), 
              Log2FC = c(-0.00357013689574257, -0.00417251481039714, 0.306809506669248, 0.224653107007472), 
              Adj.P.Value = c(0.988865360408676, 0.981816989495127, 0.00202882891738576, 2.72576774009609e-05), 
               TimeKD = c("A", "A", "B", "B"), 
               Gene = c("HSPA5", "MYH9", "HSPA5", "MYH9")), 
               row.names = c("HSPA5", "MYH9", "HSPA51", "MYH91"), 
               class = "data.frame")

plotting code

ggplot(df, aes(x = Gene, y = Log2FC, group=TimeKD)) + 
  geom_point(aes(color = -Adj.P.Value, size = Mean.Count, shape = TimeKD), alpha = 0.5)+
  coord_flip() +
  scale_colour_gradientn(
    colours = grDevices::colorRampPalette(c("black", "cyan", "violet"))(n = 200),
    values = c(0.0, 1.0), 
    #breaks = c(0.0, 0.0001, 0.001, 0.1, 1.0), <- removes legend for some reason
    space = "Lab",
    na.value = "grey50",
    guide = "colourbar",
    aesthetics = "colour"
  )+
  scale_x_discrete(limits = rev)

output (without the breaks parameter)

Pete Kittinun

Because your Adj.P.value is numeric, you have to break it into categories first.

library(dplyr)
library(ggplot2)

df<- df %>% 
  mutate(Adj.P.Value = cut(Adj.P.Value, breaks = c(0, 0.01, 0.05, 100), labels = c("<0.01", "<0.05", ">0.05")))

ggplot(df, aes(x = Gene, y = Log2FC, group=TimeKD)) + 
  geom_point(aes(color = Adj.P.Value, size = Mean.Count, shape = TimeKD), alpha = 0.5)+
  coord_flip()