Question: EnhancedVolcano: How to coloring custom gene points in volcano plot?
1
gravatar for choijamtsm
8 months ago by
choijamtsm50
choijamtsm50 wrote:

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:

Rplot

How can I color these overlapped gene lists? thank you

enhancedvolcano • 511 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by choijamtsm50
4
gravatar for Kevin Blighe
8 months ago by
Kevin Blighe69k
Republic of Ireland
Kevin Blighe69k wrote:

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

ADD COMMENTlink written 8 months ago by Kevin Blighe69k

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

ADD REPLYlink written 8 months ago by choijamtsm50

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.

ADD REPLYlink written 8 months ago by Kevin Blighe69k
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