help for volcano plot

[Chen Qian]

Hi All,

I am new to R. Right now I am trying to plot a simple volcano plot, but got some error that I cannot fix. 

require(ggplot2)




Volcano_data$threshold = as.factor(abs(Volcano_data$logFC) > 2 & Volcano_data$P.Value < 0.05)

 

##Construct the plot object

g = ggplot(data=gene_list, aes(x=logFC, y=-log10(P.Value), colour=threshold)) +

  geom_point(alpha=0.4, size=1.75) +

  theme(legend.position = "none") +

  xlim(c(-5, 5)) + ylim(c(0, 5)) +

  xlab("log2 fold change") + ylab("-log10 p-value")

g

The error is: Error in eval(expr, envir, enclos) : object 'threshold' not found. Anybody can help me with it? Thanks a lot. ---Chen



















[Julio Rojas]

Dear Qian,

It seems that you are using 

data=gene_list

instead of

data=Volcano_data

"Threshold" is defined in the second one.

Hope it helps.

-------------------------------------------------
Julio Rojas
jcred...@gmail.com

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[Chen Qian]

Thank you all for the reply. I correct the error about volcano_data, but it still did not work. Attached is the file I am working with. 

volcano_data = read.table("Volcano plot2.txt", header = T, sep = "")

require(ggplot2)

##Highlight genes that have an absolute fold change > 2 and a p-value < Bonferroni cut-off

volcano_data$threshold = as.factor(abs(volcano_data$Log2) > 1 & volcano_datat$Logo > 1.2)

##Construct the plot object

g=ggplot(data=volcano_data, aes(x=Log2, y=Logo, colour= factor(threshold)) +

  geom_point(alpha=0.4, size=1.75) +

  theme(legend.position = "none") +

  xlim(c(-4, 4)) + ylim(c(0, 5)) +

  xlab("log2 fold change") + ylab("-log10 p-value")

g  

[Dennis Murphy]

You had a couple of typos in your code. Here is a modified version
that adds some color saturation, changes the default theme to B-W and
modifies the axis labels to subscript the log bases. Delete the
theme_bw() line to get the original theme back, and remove the
scale_colour_manual() line to retrieve the original color set.

volcano_data = read.table("Volcano plot2.txt", header = TRUE, sep = "")
volcano_data <- transform(volcano_data,
threshold = as.factor(abs(volcano_data$Log2) > 1 & volcano_data$Logo > 1.2)

##Construct the plot object
g=ggplot(data=volcano_data, aes(x=Log2, y=Logo, colour= threshold)) +
theme_bw() +

geom_point(alpha=0.4, size=1.75) +
theme(legend.position = "none") +
xlim(c(-4, 4)) + ylim(c(0, 5)) +

xlab(expression(log[2]~"fold change")) +
ylab(expression(-log[10]~"p-value")) +
scale_colour_manual(values = c("firebrick", "navy"))
g

Dennis