plot_peak {FunChIP} | R Documentation |
Plotting the peaks.
Description
It plots the peaks both as counts and splines (if provided).
Peaks are centered
around their summit. If the clustering has been performed, peaks can be aligned and
divided in cluster, shown in different panels.
Usage
## S4 method for signature 'GRanges'
plot_peak(object, index = 1:length(object),
line.plot = "spline", col = NULL,
shift = NULL, k = NULL, cluster.peak = FALSE, rescale = FALSE,
lwd= 2, cex.axis = 1, cex.lab = 1, cex.main = 1)
Arguments
object |
GRanges object of length N. It must contain the metadata column counts .
If it contains the metadata column summit_spline , peaks are plotted centered around their summits
(i.e. the 0 of the abscissa is fixed as the summit of the peak). If summit is not
provided peaks are not centered.
|
index |
vector. Indices of the peaks to be plotted. Default is 1:length(object)
to plot all the peaks.
|
line.plot |
string. Type of plot. If 'spline' (default), the spline approximation of the
peaks is plotted. If 'counts' , only the raw data are plotted. If 'both' , both the
raw data and the approximation spline are plotted.
|
col |
vector. Colors used to plot the peaks. If NULL , the
rainbow color palette is used. If it has a single value, all the peaks are
plotted with the same color. If it is a vector shorter than N,
only the first element of col is used. Default is NULL .
|
shift |
logical. This parameter controls the abscissae of the
plotted peaks, and plays two different roles, depending on the cluster.peak
parameter. \
If cluster.peak is FALSE , shift = TRUE means that
peaks are plotted aligned
around the summit_spline point. The GRanges object must
contain the results of the summit_peak method.
If cluster.peak is FALSE and shift = FALSE ,
peaks are plotted with no centering around the summit. If cluster.peak is FALSE and shift = NULL (default), peaks are
centered, if the metadata column summit_spline is present in object ,
otherwise they are plotted with the original abscissae, with no centering around the summit. \
If cluster.peak = TRUE ,
the parameter shift sets the clustering result to be plotted.
If TRUE the shift results are plotted, otherwise the
results associated to NOshift clustering are presented.
|
k |
integer. If cluster.peak = TRUE ,
results corresponding to k number of clusters are plotted.
It must be set to a value included in the n.clust parameter
of the correspondent object .
|
cluster.peak |
logical. It FALSE , object contains the set of
peaks to be plotted without classification (centered or not around the
summit). If TRUE , the plot_peak method plots the result
of the classification associated to shift and k parameters;
in this case, object must be
the output of the cluster_peak
and must contain the correspondent classification. Default is FALSE .
|
rescale |
logical. If TRUE the scaled peaks are plotted. Default is
FALSE . If rescale = TRUE only spline approximations can be shown, then
line.plot must be 'spline' .
|
lwd, cex.axis, cex.lab, cex.main |
Optional graphical parameters.
|
Value
Graphical method to graphically represent data. No output returned,
Author(s)
Alice Parodi, Marco J. Morelli, Laura M. Sangalli, Piercesare Secchi, Simone Vantini
Examples
# load the data
data(peaks)
# First example:
# plot of the spline approximation
# of the first 10 peaks
# centered around their summit
plot_peak(peaks.data.summit, index = 1:10,
shift = TRUE)
# Second example:
# plot of the peaks
# divided in the k=3
# and shift = TRUE clusters
# obtained with the cluster_peak method
plot_peak(peaks.data.cluster,
shift = TRUE, k = 3, cluster.peak = TRUE)
[Package
FunChIP version 1.19.0
Index]