Entering edit mode
3.2 years ago
aranyak111
•
0
I am trying to generate a series of volcano plots of differentially expressed genes. The code snippet I am using is based on https://biocorecrg.github.io/CRG_RIntroduction/volcano-plots.html.
The exact code I am using is
data <- read.delim("E:/KDR-mir150 12.02.2021/KDR150diff.txt")
> View(data)
> p <- ggplot(data=data, aes(x=log2FoldChange, y=-log10(padj))) + geom_point() + theme_minimal()
Error in ggplot(data = data, aes(x = log2FoldChange, y = -log10(padj))) :
could not find function "ggplot"
>
> library(ggplot2)
> p <- ggplot(data=data, aes(x=log2FoldChange, y=-log10(padj))) + geom_point() + theme_minimal()
> p2 <- p + geom_vline(xintercept=c(-0.6, 0.6), col="red") +
+ geom_hline(yintercept=-log10(0.05), col="red")
> data$diffexpressed[data$log2FoldChange > >= 1 & data$pvalue < 0.05] <- "UP"
Error: unexpected '>=' in "data$diffexpressed[data$log2FoldChange > >="
> data$diffexpressed[data$log2FoldChange >= 1 & data$pvalue < 0.05] <- "UP"
> data$diffexpressed[de$log2FoldChange <= -1 & data$pvalue < 0.05] <- "DOWN"
Error in de$log2FoldChange : object of type 'closure' is not subsettable
> data$diffexpressed[data$log2FoldChange <= -1 & data$pvalue < 0.05] <- "DOWN"
> p <- ggplot(data=data, aes(x=log2FoldChange, y=-log10(padj), col=diffexpressed)) + geom_point() + theme_minimal()
> p2 <- p + geom_vline(xintercept=c(-0.6, 0.6), col="red") +
+ geom_hline(yintercept=-log10(0.05), col="red")
> p3 <- p2 + scale_color_manual(values=c("blue", "black", "red"))
>
> mycolors <- c("blue", "red" )
> names(mycolors) <- c("DOWN", "UP")
> p3 <- p2 + scale_colour_manual(values = mycolors)
> data$delabel <- NA
> data$delabel[data$diffexpressed != "NO"] <- data$genename[data$diffexpressed != "NO"]
> ggplot(data=data, aes(x=log2FoldChange, y=-log10(padj), col=diffexpressed, label=delabel)) +
+ geom_point() +
+ theme_minimal() +
+ geom_text()
> library(ggrepel)
> ggplot(data=data, aes(x=log2FoldChange, y=-log10(padj), col=diffexpressed, label=delabel)) +
+ geom_point() +
+ theme_minimal() +
+ geom_text_repel() +
+ scale_color_manual(values=c("blue", "red")) +
+ geom_vline(xintercept=c(-0.6, 0.6), col="red") +
+ geom_hline(yintercept=-log10(0.05), col="red")
I want to have all the plots scaled by the same value on the y-axis to make proper comparisons. Where in the code I need to introduce the change to make the y-axis values uniform.