Description Usage Arguments Value See Also Examples
View source: R/plot_polyviolinr.R
Plots a violin plot showing the gene-score distribution of the enriched gene sets/pathways above a give q-value and/or p-value cutoff(s)
1 2 3 4 5 6 7 8 | plot_polyviolinr(
polylinkr.out,
set.info,
obj.info,
set.obj,
p.cutoff = 0,
q.cutoff = 0
)
|
polylinkr.out |
data.table: output of polylinkr function |
set.info |
data.frame: four required fields; gene IDs, associated scores, chromosome, and start position |
obj.info |
data.frame: two required fields; genomic regions and associated scores |
set.obj |
data.frame: two required fields; genomic regions and associated scores |
p.cutoff |
float: desired p-value enrichement cutoff |
q.cutoff |
float: desired q-value enrichement cutoff |
Returns a ggplot object.
polylinkr
, PolyLinkR_SetInfo
, PolyLinkR_SetObj
, Anatolia_EF_CLR
1 2 3 4 | output = (obj.info = Anatolia_EF_CLR, set.info = PolyLinkR_SetInfo,
set.obj = PolyLinkR_SetObj, n.cores = 8, emp.nruns = 1000, NN = 10000)
p = plot_polyviolinr(polylinkr.out = output, obj.info = Anatolia_EF_CLR,
set.info = PolyLinkR_SetInfo, set.obj = PolyLinkR_SetObj, p.cutoff = 0.001)
|
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