Volcano plot interpretation

Question

[fahim]

I make a volcano plot but instead of visualizing gene symbol, it appears numbers in the plot? How can I remove the number or visualize the symbol instead of numbers? I also want to calculate the amount of upregulated and downregulated genes from them. How can I do that?I used EnhancedVolcano packages of R to make it

[Ram]

Why does your question have the blog tag?

[Kevin Blighe]

Hi! Please show the code that you have used. Also, please show a sample of your input results table. Thank you!

[fahim]

This is the code i have used

EnhancedVolcano(exp1, x = "logFC", y = "adj.P.Val",
                lab = rownames(exp1),
                FCcutoff = 0.6, pCutoff=0.01, cutoffLineType = 'twodash',
                cutoffLineWidth = 0.4, pointSize = 1, legendPosition = 'none',
                title = "", subtitle = "", caption = "", labSize = 3, ylim = c(0, 6)) +
  theme_pubr(legend = "none")

I tried to load the png file but i cannot uploaded.Moreover i cannot find the option for uploading the sample info.

[Kevin Blighe]

You have to ensure that the rownames of exp1 are set to gene names. Please verify what are the rownames. The labels used by EnhancedVolcano are whatever you pass to the lab parameter.

[fahim]

Error in rownames(Gene.symbol) : object 'Gene.symbol' not found.

[Ram]

What is this supposed to tell us? Why are you running this line of code?

[fahim]

Really very sorry for this line of code.I should write this elaborately.I mean to say when i gave lab = rownames(Gene) , [Error in rownames(Gene) : object 'Gene' not found]-This kind of error hase been shown in consol

[Ram]

And what is Gene? How are your commands related to exp1?

[fahim]

In the exp1 dataset there are 8 columns,the first one is the gene symbol column that means in that column all are gene related to my work.The second,third,fourth are logfc,adj.p.val,p val,etc.....

[Ram]

You need to use rownames(exp1) <- exp1$Gene, because you're setting rownames from a column.

[fahim]

it works but i want to remove the gene name from there because it showed very cluster together. I want to show only the colouring plot there only .So how can i do that???Moreover i want to change the color of upregulated and downregulated gene.So that i can show them very easily

[Ram]

Read the vignette and try options that make sense. In any computer science related field, this sort of trial and error and figuring out phrases to Google are of high importance. For example, you would Google "up-regulated down-regulated different colors EnhancedVolcano" for one of your requirements and "EnhancedVolcano don't show labels" for another. That should start giving you leads.