Generate a volcano plot contrasting p-value with fold change (on the
log scale), in order to visualize the effect of filtering on overall
variance and also assign significance via p-value.
The overall standard deviation filter statistics, i.e., the
square roots of the overall variance filter statistics.
n1
Sample size for group 1.
n2
Sample size for group 2.
alpha
Significance cutoff used for p-values.
S_cutoff
Filter cutoff used for the overall standard deviation in S.
cex
Point size for plotting.
pch
Point character for plotting.
xlab
Label for x-axis.
ylab
Label for y-axis.
cols
A vector of three colors used for plotting. These correspond to
filtered data, data which pass the filter but are insignificant, and
data pass the filter and are also statistically significant.
ltys
The induced bound on log-scale fold change is plotted, as is the
significance cutoff for data passing the filter. The ltys
argument gives line styles for these drawing these two thresholds on
the plot.
use_legend
Should a legend for point color be produced?
...
Other arguments for plot.
Author(s)
Richard Bourgon <bourgon@ebi.ac.uk>
Examples
# See the vignette: Diagnostic plots for independent filtering