Enrichment vignette: change from pie-charting p-val to pie chart of -log(pval)

[yochannah]

https://bioconductor.org/packages/release/bioc/vignettes/InterMineR/inst/doc/Enrichment_Analysis_and_Visualization.html#piechart-and-barplot-graphs

Pies and bar charts are pretty, but given the fact that a smaller P value is better, it takes some figuring out to understand what's going on - the smaller the pie segment / the smaller the bar, the more significant it is.

One option could be to subtract all the values from 1 so smaller values get bigger slices, but that would also require some explaining. I think it might make more sense just to remove these two visualisations.

[rachellyne]

Yep, you don't have to use the p-value. I think you can set the orderby to other things like geneNum. I think that's what we do in the Python tutorial for similar graphs and what we did last time.

[splaisan]

or use -log(pval) like in many other plots out there! :-)

[yochannah]

@splaisan that would make a lot more sense, too!

[yochannah]

I've added the hacktoberfest label to this - interested contributors, if you're interested in helping out, the chart in question is here: https://github.com/intermine/InterMineR/blob/master/vignettes/Enrichment_Analysis_and_Visualization.Rmd#L300

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