Generate MA and scatter plots of differential binding analysis results

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Description

Generates MA and scatter plots of differential binding analysis results.

Usage

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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

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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)