volcanoStatsTable {sparrow} | R Documentation |
You can, in theory, create a volcano plot from a number of different parts
of a SparrowResult()
object. Most often you want to create a volcano
plot from the differential expressino results, but you could imagine
building a volcan plot where each point is a geneset. In this case, you
would extract the pvalues from the method you like in the
SparrowResult()
object using the stats
parameter.
volcanoStatsTable( x, stats = "dge", xaxis = "logFC", yaxis = "pval", idx = "idx", xtfrm = identity, ytfrm = function(vals) -log10(vals) )
x |
A |
stats |
One of |
xaxis, yaxis |
the column of the the provided (or extracted)
|
idx |
The column of the |
xtfrm |
A function that transforms the |
ytfrm |
A function that transforms the |
Like the volcanoPlot()
function, this is mostly used by the
sparrow.shiny package.
a data.frame
with .xv
, .xy
, .xvt
and
.xvy
columns that represent the xvalues, yvalues, transformed
xvalues, and transformed yvalues, respectively
mg <- exampleSparrowResult() v.dge <- volcanoStatsTable(mg) v.camera <- volcanoStatsTable(mg, 'camera')