Hello everyone!
I am learning to create a volcano plot by using EnhancedVolcano in R. But I am struggling to color custom points (genes).
Here is my input file:
library('EnhancedVolcano')
res <- read.table("text.txt", header=TRUE)
res$gene <- as.character(res$gene)
res object contains:
head(res)
# gene log2foldchange pvalue padj
#1 Cx3cr1 -8.039239 1.29e-118 2.780000e-116
#2 Trem1 -5.258502 3.01e-44 1.770000e-42
#3 Serpina3f 3.202818 2.12e-09 2.400000e-08
Also, I have gene lists which I want to label(able to do it), and color (cannot do it) in "res$gene" object (overlapping):
gene_list <- scan("503-5ptarget.txt", what="", sep="\n")
[1] "gene" "Fam122A" "Ccnd2" "Usp2" "Arl2" "Rab9B" "Dcaf7" "Pom121" "Ccdc42B" "N4Bp1" "Tmem74B" "Akt3"
Now I created this volcano plot by injecting "gene_list" into "res$gene". But the problem was I can "label" overlapped gene, But I "cannot color that point".
aa2 <- EnhancedVolcano(res,
lab = res$gene,
x = 'log2foldchange',
y = 'pvalue',
title = 'test',
subtitle = "test",
pCutoff = FALSE,
FCcutoff = FALSE,
xlim = c(-10, 10),
pointSize = 2.0,
cutoffLineType = 'blank',
selectLab = gene_list,
labCol = 'black',
labFace = 'bold',
colAlpha = 1,
shade = gene_list,
shadeLabel = 'gene list 1',
shadeAlpha = 1/2,
shadeFill = 'red',
shadeSize = 1,
shadeBins = 5,
col = c('grey', 'grey','grey', 'grey'),
drawConnectors = TRUE,
gridlines.major = FALSE,
gridlines.minor = FALSE,
legendVisible = FALSE)
Here is the plot:
How can I color these overlapped gene lists? thank you
•
written
by
choijamtsm
Hey,
If you want to label specific genes, then you just need to use the selectLab parameter, as elaborated here:
If you want to customise the colouring of the points, then you need to follow:
A much easier way to colour-mark key genes is by following this section (but this is a relatively new feature and is not fully developed to my liking):
Kevin
I followed vignette carefully but still no luck. Is there any alternative solutions to coloring point?
A good practice is to run through the entire vignette using the code provided [in the vignette] - you literally will not have to write any of your own code. In this process, by checking the input and output for various commands / functions, you should be able to adapt the vignette's code to your own analysis.
Aren't you better off building the plot yourself? I don't think it's going to be much more complicated...
Some dummy data:
library(data.table) # Not necessary but super-useful
library(ggrepel) # This is to avoid labels overalapping each other
library(ggplot2)
gene_list <- data.table(
gene= c('gene001', 'gene002', 'gene003', 'gene004'),
colour= c('red', 'blue', 'orange', 'violet')
)
set.seed(123)
n <- 1000
res <- data.table(
gene= sprintf('gene%03d', 1:n),
log2foldchange= c(rgamma(n/2, 1, 2), -rgamma(n/2, 1, 2)),
padj= 10^-rgamma(n, 1, 0.1)
)
Convert padj to -log10(p) and add colour choice:
res[, log10padj := -log10(padj)]
res <- merge(res, gene_list, by= 'gene', all.x= TRUE)
res
gene log2foldchange padj colour log10padj
1: gene001 0.09110855 1.553255e-11 red 10.808757
2: gene002 0.84787557 5.187897e-30 blue 29.285009
3: gene003 0.81044009 1.754765e-15 orange 14.755781
4: gene004 1.22404803 3.007857e-03 violet 2.521743
5: gene005 0.43951396 4.294535e-20 <NA> 19.367084
---
996: gene995 -0.74794774 8.898109e-04 <NA> 3.050702
997: gene996 -0.28476577 4.175561e-10 <NA> 9.379285
998: gene997 -0.09387140 1.521622e-04 <NA> 3.817693
999: gene998 -0.99570414 1.755187e-02 <NA> 1.755677
1000: gene999 -0.73455174 2.145441e-12 <NA> 11.668483
Plot with various bells and whistles:
gg <- ggplot(data= res, aes(x= log2foldchange, y= log10padj, label= gene)) +
geom_point(colour= 'grey80') +
geom_point(data= res[abs(log2foldchange) > 0.5 & log10padj > 2], colour= 'grey30') +
geom_point(data= res[!is.na(colour)], colour= 'orange') +
geom_vline(xintercept= c(-0.5, 0.5), colour= 'blue', linetype= 'dashed') +
geom_hline(yintercept= 2, colour= 'blue', linetype= 'dashed') +
geom_text_repel(data= res[!is.na(colour)], colour= colour, fontface= 'bold') +
xlab('log2 fold-change') +
ylab('-log10(Padj)') +
theme_classic()
ggsave('tmp.png', width= 12, height= 12, units= 'cm')
There may be different and probably better ways of doing it but hoepfully you get the idea...
aún mejor / meglio:
plot(x, -log10(y))
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I followed vignette carefully but still no luck. Is there any alternative solutions to coloring point?
Please use
ADD COMMENT/ADD REPLYwhen responding to existing posts to keep threads logically organized. This comment belongs under @Kevin's answer.SUBMIT ANSWERis for new answers to original question.Hi, I have the same problem than "choijamtsm", i followed the script and i'm able to put its specific name but i don't known how to change the color of a specific point, this will be very useful for me. thanks in advance
Can you please share the code that you have already tried? Also, please show samples of your input data (the results table)