VolcanoPlot: Draw a Volcano plot.
In jvanheld/stats4bioinfo: Utilities for the book "Statistics for bioinformatics"

Description Usage Arguments Value Author(s)

Draw a volcano plot from a table containing at least one column for the effect size, and another one for the p-value or an equivalent measure of significance (FDR, e-value, FWER, ...).

VolcanoPlot(multitest.table, effect.size.col, control.type = "p.value",
  nb.tests = nrow(multitest.table), alpha = 0.05, effect.threshold = NULL,
  sort.by.pval = FALSE, plot.points = TRUE, plot.ci = FALSE,
  xlab = "Effect size", ylab = paste(sep = "", "-log10(", control.type,
  ")"), density.colors = FALSE, col.points = "#888888",
  col.positive = "#4455DD", col.grid = "#AAAAAA", col.lines = "blue",
  col.alpha = "darkred", lty.lines = "solid", lty.alpha = "dashed",
  lty.grid = "dotted", pch.positive = 3, pch.negative = 1, xlim = NULL,
  ylim = NULL, cex = 0.6, legend.corner = "bottomleft",
  full.legend = FALSE, legend.cex = 1, tick.size = 0.05, ...)

`effect.size.col`	A column number or name, inidicating which column of the result table contains the effect size, which will be
`xlim`	Range of the X axis.
`ylim`	Range of the Y axis.
`...`	Additional parameters are passed to plot()
`result.table`	A data frame containing one row per feature, and one column per statistics.
`control.type="p.value"`	A column number or name, indicating which column of the result table contains the p-value or an equivalent indication of the significance of each feature (example: "fdr", "e.value", "p.value")
`nb.tests=nrow(multitest.table)`	Total number of tests performed (by default, the number of rows in the table).
`alpha=0.05`	Alpha threshold for the control of false positives
`effect.threshold=NULL`	Threshold on the absolute value of the effect size.
`sort.by.pval=FALSE`	Sort row by p-value in order to plot significant elements on top of non-significant
`xlab="Effect`	size" Label for the X axis.
`ylab="sig`	= -log10(p-value)" Label for the Y axis
`density.colors=FALSE`	Automatically set the colors according to feature status and local density in the Volcano space.
`col.points='#888888'`	Color(s) for the points. can be either a single value (same color for all points), or a vector of the same length as the numer of genes (rows) of the input table.
`col.positive='#4455DD'`	Color to highlight significant points (called positive). When NULL, positive points are not displayed.
`col.lines='blue'`	Color for the line highlighting the effect size thresholds.
`col.alpha="darkred"`	Color for the line highlighting the significance threshold.
`col.grid='#AAAAAA'`	Grid color
`lty.lines="solid"`	Line type for the lines.
`lty.alpha="dashed"`	Line type for the horizontal line denoting the alpha theshold.
`lty.grid="dotted"`	Line type for the grid.
`pch.positive=3`	Point shape for the positive tests (default: 3, i.e. + symbol)
`pch.negative=1`	Point shape for the negative tests (default: 1, i.e. o symbol)
`legend.corner="bottomleft"`	Corner for the legend. When NULL, no legend is displayed.
`full.legend=TRUE`	Plot additional indications on the legend (number of elements passing the different adjusted p-values)
`legend.cex=1`	Font size for the legend.
`cex=0.6`	Point size, passed to plot() and lines()
`plot.points=TRUE`	Plot one point per row with the significance (sig=-log10(p-value)) as a function of the effect size.
`plot.ci=FALSE`	Plot horizontal bars to denote confidence intervals around the mean difference.
`tick.size=0.05`	Height of the vertical lines denoting the boundaries of confidence intervals.