Entering edit mode
3.3 years ago
peter.berry5
▴
60
I'm using the Enhanced Volcano package to represent my DE proteins on a volcano plot. Drawing the plot isn't an issue but selectively labeling points of interest is. According the the package vignette the necessary code is
EnhancedVolcano(res,
lab = rownames(res),
x = 'log2FoldChange',
y = 'pvalue',
selectLab = c('TMEM176B','ADH1A'),
xlab = bquote(~Log[2]~ 'fold change'),
pCutoff = 10e-14,
FCcutoff = 2.0,
pointSize = 4.0,
labSize = 6.0,
shape = c(4, 35, 17, 18),
colAlpha = 1,
legendPosition = 'right',
legendLabSize = 14,
legendIconSize = 5.0)
My code is
EnhancedVolcano(volcano_rd,
lab = 'volcano_rd$DE_Proteins',
x = 'log2FC',
y = 'pvalue',
xlim = c(-5, 5),
ylim = c(0, 8),
selectLab = c('RRP1B', 'PLIN2'),
xlab = bquote(~Log[2]~ 'FC'),
pointSize = 3.0,
labSize = 6.0,
pCutoff = 0.0001,
FCcutoff = 1.2,
cutoffLineType = 'twodash',
cutoffLineWidth = 0.8,
col=c('orange', 'green','pink', 'blue'),
colAlpha = 1,
legendPosition = 'right',
legendLabSize = 16,
legendIconSize = 5.0)
dev.off()
I think the issue is with the line
`xlab = bquote(~Log[2]~ 'FC')`,
but I don't understand what this line does and don't know what to change.
My data looks like this
str(volcano_rd)
'data.frame': 1191 obs. of 4 variables:
$ pvalue : num 0.007987 0.000869 0.00104 0.001904 0.003591 ...
$ log2FC : num 0.481 0.383 0.766 0.595 0.773 ...
$ FC : num 1.4 1.3 1.7 1.51 1.71 ...
$ DE_Protein: chr "AAAS" "AARS" "ABCB6" "ABCB7" ...
and the two points I want to label are present in the data and exceed the cutoff I have set for PCutoff and FCcutoff
Any suggestions would be appreciated.
Peter