dba.plotMA {DiffBind} | R Documentation

## Generate MA and scatter plots of differential binding analysis results

### Description

Generates MA and scatter plots of differential binding analysis results.

### Usage

    dba.plotMA(DBA, contrast=1, method=DBA$config$AnalysisMethod,
               th=DBA$config$th, bUsePval=DBA$config$bUsePval,
               fold=0, bNormalized=TRUE,
               factor="", bFlip=FALSE, bXY=FALSE, dotSize=.45,
               bSignificant=TRUE, bSmooth=TRUE,
               xrange, yrange, ...)

### 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; all 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).
`bNormalized` | logical indicating whether to plot normalized data using normalization factors computed by differential analysis method (TRUE) or raw read counts (FALSE).
`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.
`bXY` | logical indicating whether to draw MA plot (FALSE) or XY scatter plot (TRUE).
`dotSize` | size of points on plot (cex).
`bSignificant` | Logical indicating if points corresponding to significantly differentially bound sites (based on `contrast`, `th`, `bUsePval`, and `fold` parameters) should be overlaid in red.
`bSmooth` | logical indicating that basic plot should be plotted using `smooth Scatter`. Note that overlaid significant sites will be not plotted using a smoothing function.
`xrange` | vector of length 2 containing the desired minimum and maximum concentrations to plot.
`yrange` | vector of length 2 containing the desired minimum and maximum fold changes to plot.
`...` | passed to plot.

### Author(s)

Rory Stark

### See Also

`dba.analyze`

### Examples

    data(tamoxifen_analysis)

    # default MA plot
    dba.plotMA(tamoxifen)

    #XY plots (with raw and normalized data)
    par(mfrow=c(1,2))
    dba.plotMA(tamoxifen,bXY=TRUE,bSmooth=FALSE,bNormalized=FALSE)
    dba.plotMA(tamoxifen,bXY=TRUE,bSmooth=FALSE,bNormalized=TRUE)

[Package DiffBind version 2.10.0 Index]