dba.plotVolcano {DiffBind} | R Documentation

## Generate volcano plots of differential binding analysis results

### Description

Generates volcano plots of differential binding analysis results.

### Usage

    dba.plotVolcano(DBA, contrast=1, method=DBA$config$AnalysisMethod,
                                th=DBA$config$th, bUsePval=DBA$config$bUsePval,
                                fold=0, factor="", bFlip=FALSE,
                                bLabels=FALSE, maxLabels=50, dotSize=1)

### Arguments

`DBA` | DBA object, on which `dba.analyze` should have been successfully run.

`contrast` | number of contrast to report on. See `dba.show(DBA, bContrast=TRUE)` to get contrast numbers.
`method` | method or vector of methods to plot results for: `DBA_DESEQ2` `DBA_DESEQ2_BLOCK` `DBA_EDGER` `DBA_EDGER_BLOCK`
`th` | significance threshold; sites with FDR (or p-values, see `bUsePval`) less than or equal to this value will be colored red in the plot
`bUsePval` | logical indicating whether to use FDR (`FALSE`) or p-value (`TRUE`) for thresholding.
`fold` | will only include sites with fold change greater than this as significant (colored red).
`factor` | string to be prepended to plot main title; e.g. factor name.
`bFlip` | logical indicating that order of groups in contrast should be "flipped", allowing control of which sample group will have positive and which will have negative fold changes.
`bLabels` | logical indicating that labels should be drawn on the plot. The labels are the site numbers, the row index in the (silently) returned set of significant sites. The maximum number of sites can be specified using `maxLabels`.
`maxLabels` | The maximum number of labels to use in the plot. Ignored if `bLabels=FALSE`.
`dotSize` | size of points on plot.

### Details

Makes a volcano plot.

### Value

silently returns a `GRanges` object of the sites highlighted in red.

### Author(s)

Rory Stark

### See Also

`dba.analyze`, `dba.plotMA`

### Examples

    data(tamoxifen_analysis)

    # default volcano plot
    dba.plotVolcano(tamoxifen)

    # only highlight significant sites with at least 5x Fold Change
    sigSites <- dba.plotVolcano(tamoxifen, fold=log2(5))

    # use labels to find outlier sites
    sigSites <- dba.plotVolcano(tamoxifen, fold=log2(10),bLabels=TRUE)
    sigSites

[Package DiffBind version 3.2.7 Index]