Scatter plot of DEG in R

Question

[ATCG]

Hello, I apologize for the basic question. How can I generate a scatter plot of DEG in R, as shown in this example? Specifically, if you can suggest a line of code I can use to label up=red and down=blue.

Thanks in advance for your help!

Answer 1

[ATpoint]

Basically something lime this:

#/ Create some dummy data:
library(DESeq2)
Counts  <- log10(assay(makeExampleDESeqDataSet(n=5000, m = 2), "counts")+1)
df <- data.frame(Counts=Counts)
colnames(df) <- c("sample1", "sample2")
df$status <- "NS"
classify <- (df$sample1+1) - (df$sample2+1)
df$status[classify > 0.5] <- "up"
df$status[classify < (-0.5)] <- "down"

#/ Make the basic plot
library(ggplot2)
df %>%
  ggplot(aes(x=sample1, y=sample2, color=status)) + 
  geom_point() +
  scale_color_manual(labels=c("down", "NS", "up"), values=c("firebrick", "grey", "dodgerblue"))

You will probably want to read on the basics of ggplot2 to understand the code as simply copy/pasting it will not have much of a learning benefit. There are plenty of tutorials out there for this, it is an excellent investment of time to understand ggplot2.

Maybe check out Volcano plots, or MA-plots as an alternative to present your results, e.g. https://bioconductor.org/packages/release/bioc/vignettes/EnhancedVolcano/inst/doc/EnhancedVolcano.html which is relatively intuitive to use and it does all the ggplot-ing under the hood for you. Once you get the grasp of ggplot2 you can write custom code if you do not like the look of the plots this package (or any other) produces.

[ATCG]

I am familiar with volcano plots and MA-plots and agree that these are probably better plots for presenting DEG. This is wonderful!! Thank you so much, you are the best!!