R/volcano_plot.R
volcanoStatsTable.RdYou 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)
)A SparrowResult object, or a data.frame
One of "dge" or resultNames(x)
the column of the the provided (or extracted)
data.frame to use for the xaxis and yaxis of the volcano
The column of the data.frame to use as the identifier
for the element in the row. You probably don't want to mess with this
A function that transforms the xaxis column to an
appropriate scale for the x-axis. This is the identity function
by default, because most often the logFC is plotted as is.
A function that transforms the yaxis column to an
appropriate scale for the y-axis. This is the -log10(yval) function
by default, because this is how we most often plot the y-axis.
a data.frame with .xv, .xy, .xvt and
.xvy columns that represent the xvalues, yvalues, transformed
xvalues, and transformed yvalues, respectively
Like the volcanoPlot() function, this is mostly used by the
sparrow.shiny package.
mg <- exampleSparrowResult()
v.dge <- volcanoStatsTable(mg)
v.camera <- volcanoStatsTable(mg, 'camera')