dba.plotMA {DiffBind} | R Documentation |
Generates MA and scatter plots of differential binding analysis results.
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, ...)
DBA |
DBA object, on which |
contrast |
number of contrast to report on. See |
method |
method or vector of methods to plot results for: |
th |
significance threshold; all sites with FDR (or p-values, see |
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 |
bSmooth |
logical indicating that basic plot should be plotted using |
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. |
Rory Stark
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)