[R] Volcano Plot

[Martin Morgan]

On 02/28/2012 08:13 AM, aishsk wrote:
> Hi I am using the ggplot2 package for the volcano plot and I am using the
> following code for the same:
>
> g = ggplot(data=data, aes(x=data[11], y=-log10(data[12]), colour=threshold))
> +
> +   geom_point(alpha=0.4, size=1.75) +
> +   opts(legend.position = "none") +
> +   xlim(c(-10, 10)) + ylim(c(0, 15)) +
> +   xlab("log2 fold change") + ylab("-log10 p-value")
>
> data[11] is a column of the fold change values and data[12] contains the P
> values and I am getting a following error:
>
> Error: geom_point requires the following missing aesthetics: x, y
>   What can be done for the same ?
> And if not what other package may I use for the same in which I don't have
> to use a lmfit model?

Have you tried, if 'data' is a data.frame, simply plot(data[[1]], 
-log10(data[[12]])) ?

Martin

> Thanks
>
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