volcanoplot_topTable: A topTable volcano plot. Volcano plot of a toptable - similar...
In drmjc/microarrays: A collection of microarray and genomic helper code.

Description Usage Arguments Value Author(s)

A topTable volcano plot. Volcano plot of a toptable - similar to volcanoplot from limma, but more flexible in terms of what is plotted on the y-axis.

  volcanoplot_topTable(tt, yaxis = c("p", "q", "B", "t"),
    xaxis = c("logFC", "signedFC", "FC"), yThresh = 0.05,
    lfc = log2(1.5), highlight = 0, names = tt$ID,
    main = "Volcano Plot", cex.points = 0.2, ablines = "",
    abline.col = "grey", colour.scheme = "red",
    xlim = NULL, ylim = NULL, xlab = NULL, ylab = NULL,
    do.par = TRUE, ...)

`tt`	a `data.frame` object from calling `topTable` with all genes.
`yaxis`	choose one of “p”, “q”, “B”, “t”, “absT” to plot the raw P-values, the q value (either from a column called “q”, or “adj.P.Val” in that order), the B statistics (log odds), the t-statistic, or the absolute t-statistic, respectively.
`xaxis`	the x-axis type. one of: “logFC” (default), “signedFC” (see `logFC2signedFC`), or “FC” (unlogged Fold Change)
`yThresh`	For colouring significant points. For eg, choose 0.05 for P/q, or 3 for B, or 5 for t
`lfc`	the absolute log fold change threshold. eg 0.585 for 1.5 FC, or 1.0 for a 2-fold change
`highlight`	the number of points to highlight by name
`names`	the names to use if highlight > 0. This should have as many rows as were passed into `lmFit`, and should be in the same order as the genes passed into lmFit. The tt's row names (which are numeric) will be used to index into this vector of names.
`main`	the plot title.
`cex.points`	see `par`
`ablines`	whether to add vertical dashed lines at `yThresh` and `xThresh`. “”, “x”, “y”, or “xy” for none, x (ie vertical lines at +/- xThresh only), y (ie horizontal line at yThresh only), x and y
`abline.col`	the colour of the ablines, if `ablines != ""`
`colour.scheme`	Control the higlighting of DE genes, via either black/red dots (“red”) or closed/open circles(“black”)
`xlim`	see `par` if `NULL` it will be made symmetrical so that all data points fit
`ylim`	see `par`. if `NULL` it will fit all data points
`xlab`	The x-axis label. if `NULL` it's auto-determined from `xaxis`
`ylab`	The y-axis label. if `NULL` it's auto-determined from `yaxis`
`do.par`	logical: setup the plot parameters
`...`	further arguments passed to `plot`