plotting according p-value

Question

[Sam]

Dear All

according to the genotyping by sequencing data analysis and compare them between different samples, I obtained 3 p-values for each comparison but I want to have the plot to show the loci which NOT significantly different in column 1 but they are significantly different in other columns (-log10 p-value > 2). for instance in a plot similar to volcano plot for gene expression.

p-values are transformed to -log10

Thanks for your help

      Site Name     columnA     columnB        columnC
        2632698    1.679410599  9.150306514 29.8745832
        36090354    1.679410599 9.150306514 29.8745832
        664409      2.963333465 8.704834332 16.8225854
        37630422    3.963333465 8.704834332 16.8225854

[h.mon]

A volcano plot shows the relation between two values: log2( fold change) vs log( p-values ).

You have three values, all p-values. I fail to see how to make the plot you want. You want a 3D plot?

[Sam]

could you help me to have the 3D plot for this data?

[Devon Ryan]

Why do you want to plot that? A bit of the motivation behind this would be helpful.

[Sam]

the p-value for each locus was calculated by comparison between Mendelian ration vs obtained ration from our samples and we need to plot them to show the loci which NOT significantly different in column 1 but they are significantly different in other columns, we have about 5 k loci for this analysis.

[Devon Ryan]

That's what you want to plot, not why you want to plot it.

[Sam]

we have some positions which are significant differences with the Mendelian ratio and I think the simplest way to visualize the result is showing them with a plot. du to that I mentioned to "in a plot similar to volcano plot for gene expression" to quickly identify changes in large data sets and a better showing of results.