plotWindow {ChIPseqR} | R Documentation |
Read count within a selected region of the genome are plotted, optionally together with binding site score and location of predicted binding sites.
.plotWindow(data, chr, center, score, width=2000, bind, start, end, bind.col=3, score.type='l', xlab=NULL, ylab="Read count", cutoff=TRUE, offset = 1, ...)
data |
Object of class |
chr |
A character string or numeric index identifying the the chromosome on which the region is located. |
center |
Numeric value giving the center of the region on chromosome |
score |
An object of class |
width |
Width of the window to plot. The plotted region will be [center - width/2, center + width/2]. |
bind |
Length of binding site, ignored if |
start |
Start of plotting window (may be used together with |
end |
End of plotting window (may be used together with |
bind.col |
Color used to indicate location of binding sites, ignored if |
score.type |
Plotting type to use for score, ignored if |
xlab |
X-axis label. This defaults to a description of the genomic location constructed from |
ylab |
Y-axis label. |
cutoff |
Logical indicating whether the significance threshold used to predict binding site locations should be indicated by a horizontal line in the plot. |
offset |
Position on chromosome |
... |
Further arguments to |
If 'score'
is present the binding site score is plotted on top of read counts. Scores are rescaled
to lie between 0 and the maximum number of reads in the window. A corresponding scale is added to the right
hand axis.
Called for its side effect.
Peter Humburg