Entering edit mode
2.3 years ago
LChart
4.6k
I have a gene sets, together with enrichment statistics, and the correlation of the gene set 'activity' within an expression dataset. I would like to visualize the enrichment statistics and correlations simultaneously.
It may be possible to get snp.plotter
to do this, but it's not exactly straightforward. It would be nice to do this programmatically, as opposed to editing the separate plots together post-hoc.
Input looks like
example.data.values <- data.frame(
state=c('A', 'B', 'C', 'D'),
statistic=c('3.14', '1.16', '0.28', '2.04')
)
example.data.corr <- data.frame(
state1=c('A', 'A', 'A', 'B', 'B', 'C'),
state2=c('B', 'C', 'D', 'C', 'D', 'D'),
corr=c(0.38, 0.55, 0.57, 0.10, 0.35, 0.26)
)
Desired output: something like:
Edit: Note that this is a composite image constructed in powerpoint, not a single figure, which is the desired output.
What about an UpSet plot?
UpSetR
package will do a similar plot and IMO much cleanerAn upset plot has (2^N - 1) bars, one for each possible intersection set. The statistics I have cannot be apportioned into the various intersections. Therefore, I want a specific plot to simultaneously display N points (enrichments) and (N choose 2) points (correlations / Jaccard).
It's not entirely clear to me what the issue is. Your toy example seems to give you what you want. Where's the hold up?
I had to construct my toy example by combining 2 separate plots. I want an automated process.