EnhancedVolcano: How to coloring custom gene points in volcano plot?

Question

[choijamtsm]

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

[luishernanhuertas]

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

[Kevin Blighe]

Can you please share the code that you have already tried? Also, please show samples of your input data (the results table)

Answer 1

[Kevin Blighe]

Hey,

If you want to label specific genes, then you just need to use the selectLab parameter, as elaborated here:

• 4.7 Only label key variables

If you want to customise the colouring of the points, then you need to follow:

• 4.9 Over-ride colouring scheme with custom key-value pairs

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):

• 4.11 Shade certain variables

Kevin

[choijamtsm]

I followed vignette carefully but still no luck. Is there any alternative solutions to coloring point?

[Kevin Blighe]

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.

Answer 2

[dariober]

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...

[Kevin Blighe]

aún mejor / meglio:

plot(x, -log10(y))