CODEWITHSUNDEEP
rggplot2limma
user11641357
user11641357

Reputation:

Error trying to add colours to R ggplot (volcano plot)

Wanted to make a volcano plot that was coloured based on signifcance and differential expression. Made a dataframe using toptable in R from Limma object. Added colour column to to the data frame based on adjusted p value and logfc. So each gene also had a colour assigned ("fill), then used these colours to make ggplot:

 geom_point(mapping = aes(x= logFC, y= log10adj, colour = fill))+
 geom_hline(yintercept=1.3, linetype="dashed", color = "red")+
 geom_vline(xintercept=-1, linetype="dashed", colour= "blue")+
 geom_vline(xintercept=1, linetype="dashed", colour= "blue")+
 xlab("Log2 Fold Change")+
 ylab("-Log10 Adjusted P-value")+
 xlim(-3,3)+
 theme_grey()

But then the ggplot isn't coloured properly:

Incorrect plot

If i add shape to the aesthetic i get an error:

ggplot(voom_topt)+
  geom_point(mapping = aes(x= logFC, y= log10adj, colour = fill, shape = 23))+
  geom_hline(yintercept=1.3, linetype="dashed", color = "red")+
  geom_vline(xintercept=-1, linetype="dashed", colour= "blue")+
  geom_vline(xintercept=1, linetype="dashed", colour= "blue")+
  xlab("Log2 Fold Change")+
  ylab("-Log10 Adjusted P-value")+
  xlim(-3,3)+
  theme_grey()

Error: A continuous variable can not be mapped to shape Run rlang::last_error() to see where the error occurred.

Does anyone have any idea how to resolve this? I cant figure out why this is going wrong (Ps i am quite new to R)

Thanks for any help!!

Upvotes: 0

Views: 398

Answers (1)

rg255
rg255

Reputation: 4169

You need to use scale_color_manual as so

ggplot(mtcars) +
geom_point(mapping = aes(
  x = mpg, y = wt, color = factor(cyl))) + 
scale_color_manual(values = c("red", "black", "green"))

From what I can see with your code, you would set color = factor(fill) then pass your four colors to the scale_color_manual

Upvotes: 1

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