Gene name put in volcano plot with already have file.

Question

[harry]

hi, I have an edgeR result and I want to plot the volcano plot with gene names that are differentially expressed. Can anyone help me with how I plot the volcano plot with the below result that I have? I want to select genes which are log2 FC is greater than 2 or less than 2 and pvalue<=.05 as differentially expressed.

Gene    logFC   logCPM  PValue
Gene3107    6.981105959 7.745879848 2.76E-07
Gene191 6.710771146 7.531024905 4.12E-06
Gene2930    6.691754954 7.516131826 5.21E-05
Gene14661   6.286691745 7.213119385 0.000317124
Gene10156   5.950401116 6.97738046  0.005639918
Gene15428   5.839150656 6.905392409 0.005893609
Gene2301    5.826326991 6.899054669 0.005470969
Gene3103    5.734866666 6.836369516 0.018717277
Gene2594    5.714657239 6.827703722 0.009375846
Gene4768    5.714657239 6.827703722 0.009375846
Gene7775    5.610471555 6.759350557 0.027504018
Gene9260    5.610471555 6.759350557 0.027504018
Gene13101   5.598965949 6.754904281 0.016959051
Gene6825    5.47414377  6.678155971 0.03692049
Gene2187    5.467748523 6.675873253 0.028818664
Gene45  5.467748523 6.675873253 0.028818664
Gene10212   5.461811716 6.673590674 0.025766936
Gene11933   5.461811716 6.673590674 0.025766936
Gene15985   5.461811716 6.673590674 0.025766936
Gene9828    5.461811716 6.673590674 0.025766936
Gene13663   5.449603204 6.669025954 0.035076632
Gene1718    5.449603204 6.669025954 0.035076632
Gene4425    5.449603204 6.669025954 0.035076632
Gene5392    5.449603204 6.669025954 0.035076632
Gene9642    5.449603204 6.669025954 0.035076632
Gene15899   5.442635466 6.666743825 0.048722867
Gene3243    5.442635466 6.666743825 0.048722867
Gene13478   5.323605321 6.592313207 0.049469331
Gene5832    5.323605321 6.592313207 0.049469331

Thanks in advance

Answer 1

[GenoMax]

Covered in EnhancedVolcano vignette.

[harry]

But I have to analyze the result again or I directly put my result which is saved. Which file type is used for putting the result in EnhancedVolcano and how. Thanks

[GenoMax]

Read in your result file from edgeR and use it.

[harry]

I used the following command but it gives an error:- I also upload some data of the Enhanced_volcano.csv file. .

countData <- read.csv('Enhanced_volcano.csv', header = TRUE, sep = ",") EnhancedVolcano(countData, lab = rownames(countData), x = 'log2FoldChange', y = 'pvalue') Error in EnhancedVolcano(countData, lab = rownames(countData), x = "log2FoldChange", : log2FoldChange is not numeric!

Gene    logFC   PValue
Gene3599    4.482499061 8.69E-13
Gene3600    3.655584188 6.33E-11
Gene3597    3.856439936 1.11E-07
Gene10356   -2.055105535    3.16E-07
Gene291 2.372632224 2.30E-07
Gene3107    6.981105959 2.76E-07
Gene5284    2.625716271 3.05E-07
Gene15892   2.994687682 2.07E-06
Gene191 6.710771146 4.12E-06
Gene9824    3.73240982  1.14E-05
Gene2192    -6.384105349    2.06E-05
Gene1922    -6.308628891    4.09E-05
Gene680 -1.248001293    4.46E-05
Gene14521   -6.32174007 5.38E-05
Gene2930    6.691754954 5.21E-05
Gene16651   -6.241947154    8.49E-05
Gene10757   -1.733474139    0.000146068
Gene14385   1.59603191  0.000181118
Gene11606   -6.164592068    0.000202988
Gene1705    -2.876362447    0.000242359
Gene10669   -2.863352854    0.00030307
Gene10855   -2.826417414    0.000306434
Gene12520   -2.157870239    0.000278709
Gene14661   6.286691745 0.000317124

Thanks in advance

[jack.henry]

Your csv and code do not match up. Try:

EnhancedVolcano(countData, lab = countData$Gene, x = 'logFC', y = 'PValue')