Control order across factors in ggplot2

December 7, 2022

I have a plot that looks like below. I want to change the order so that the larger value comes first (so cyan would precede red). But I can’t seem to do this. What am I doing wrong?

This is my current code block so far:

ggplot(df, aes(x = Gene.Set.Size, y = OR, label =P.value, color = Method, group = Method)) +
  geom_point(position=position_dodge(width=0.5))  +
  ggrepel::geom_text_repel(size = 6, box.padding = 1, segment.angle = 20, position=position_dodge(width=0.5))+
  geom_pointrange(aes(ymax = UpperCI, ymin = LowerCI),position=position_dodge(width=0.5)) +
  theme_bw() +
  theme(text=element_text(size=25),axis.text.x = element_text(angle = 45, hjust = 1)) +
  ylab("Odds ratio") +
  xlab("Gene set size") +
  theme(plot.margin = unit(c(2,2,2,2), "cm"))

> dput(df)
structure(list(Method = structure(c(1L, 1L, 1L, 2L, 2L, 2L), .Label = c("MAGMA", 
"Pairwise"), class = "factor"), P.value = c(8.74e-28, 1.33e-56, 
5.57e-92, 1.63e-44, 4.23e-71, 2.78e-95), OR = c(1.39, 1.424668, 
1.4, 1.513, 1.478208, 1.409563), UpperCI = c(1.481491, 1.487065, 
1.446039, 1.601557, 1.417117, 1.455425), LowerCI = c(1.316829, 
1.364601, 1.356358, 1.42, 1.541768, 1.365056), Gene.Set.Size = structure(c(1L, 
2L, 3L, 1L, 2L, 3L), .Label = c("500", "1000", "2000"), class = "factor")), row.names = c(NA, 
-6L), class = "data.frame")

>Solution :

You must set the factor order.

library(ggplot2)
df <- structure(list(Method = structure(c(1L, 1L, 1L, 2L, 2L, 2L), .Label = c("MAGMA", 
"Pairwise"), class = "factor"), P.value = c(8.74e-28, 1.33e-56, 
5.57e-92, 1.63e-44, 4.23e-71, 2.78e-95), OR = c(1.39, 1.424668, 
1.4, 1.513, 1.478208, 1.409563), UpperCI = c(1.481491, 1.487065, 
1.446039, 1.601557, 1.417117, 1.455425), LowerCI = c(1.316829, 
1.364601, 1.356358, 1.42, 1.541768, 1.365056), Gene.Set.Size = structure(c(1L, 
2L, 3L, 1L, 2L, 3L), .Label = c("500", "1000", "2000"), class = "factor")), row.names = c(NA, 
-6L), class = "data.frame")

#reorder Factor
df$Method = factor(df$Method, levels=c("Pairwise", "MAGMA"))

ggplot(df, aes(x=Gene.Set.Size, y=OR, label=P.value, 
               group= Method, color=Method)) + 
  geom_point(position=position_dodge(width=0.5))  +
  ggrepel::geom_text_repel(size = 6, box.padding = 1, segment.angle = 20, position=position_dodge(width=0.5))+
  geom_pointrange(aes(ymax = UpperCI, ymin = LowerCI),position=position_dodge(width=0.5)) +
  theme_bw() +
  theme(text=element_text(size=25),axis.text.x = element_text(angle = 45, hjust = 1)) +
  ylab("Odds ratio") +
  xlab("Gene set size") +
 theme(plot.margin = unit(c(2,2,2,2), "cm"))