GO enrichment plot with dotplot strange axis

Question

[Picasa]

Hi,

I wanted to make a simple enrichment plot:

dotplot(ego_bp, x = "p.adjust", showCategory = 20)

1)I don't understand how the showCategory argument work because I got different results each time I change it.

2) With showCategory = 20 , the x axis is strange. The 'positive regulation of inflammatory response' has a p.adjust=1*10^-8 but it is at the extreme right ... Is it a bug ? do wou have any recommendation ?

Thanks

[bk11]

I have seen plots like this. I do not think the dot on positive regulation of inflammatory response is a bug. What genes are you inputting for the GO enrichment? Looks like there are some immune regulatory genes in your input data.

[Picasa]

Yes there are some genes involved in positive regulation of inflammatory response

Do you know how showCategory work ?

[bk11]

By default, only top 5 (most significant) categories of each cluster are plotted. You can change the parameter showCategory to specify as many categories of each cluster to be plotted as you want. If you set showCategory to NULL, the whole enrichment results will be plotted. Moreover, you can also pass a vector of selected categories (pathway of interests) to plot.