Volcano plot for differential expression studies
Usage
# S3 method for numeric
volcanoPlot(
x,
y,
pval,
thr,
p = 1,
q = 1,
r = 0,
cex = c(0.2, 0.6),
col = c("#33333333", "#FF0000", "#FF666633"),
pch = 19,
ylim = NULL,
bounds = TRUE,
...
)
Arguments
- x
A vector of fold changes (x axis of the volcano plot)
- y
A vector of p-values (y axis of the volcano plot)
- pval
A vector of p-values, of the same length as
x
, use to estimate post-hoc bounds- thr
A numeric vector of length K, a JER controlling family, used to estimate post-hoc bounds
- p
A numeric value, the p-value threshold under which genes are selected
- q
A numeric value, the q-value (or FDR-adjusted p-value) threshold under which genes are selected
- r
A numeric value, the absolute fold change above which genes are selected
- cex
A numeric vector of length 2, the relative magnification factor for unselected (
cex[1]
) and unselected (cex[2]
) genes.- col
A vector of length 3
- pch
An integer or single character string specifying the plotting character, see
par
- ylim
A numeric vector of length 2, the \(y\) limits of the plot
- bounds
A boolean value: should the post hoc bounds be displayed on the plot? Defaults to TRUE
- ...
Not used
Details
A Welch T-test of differential expression between the two categories
defined by categ
are applied for each gene using the
rowWelchTests
function, which also outputs the "fold change"
(mean difference in log scale) between the two categories.
See also
Volcano plot shiny app at https://shiny-iidea-sanssouci.apps.math.cnrs.fr/