plot: Generic plot function for SeqPlots package calsses

In seqplots: An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps

Description

Generic plot function for SeqPlots package calsses

Usage

plot(x, y, ...)

## S4 method for signature 'PlotSetPair,ANY'
plot(x, what = "a", ...)

## S4 method for signature 'PlotSetList,ANY'
plot(x, what = "a", ...)

## S4 method for signature 'PlotSetArray,ANY'
plot(x, what = "a", ...)

Arguments

x	This argument should be one of SeqPlots classes: PlotSetArray, PlotSetList or PlotSetPair
y	For plotting SeqPlots classes this argument is ignored, used for default functionality of plot function.
...	Other parameters controlong the plot, see plotAverage for avareange plot and plotHeatmap for heatmaps.
what	This argument takes a character determining if avareange plot ("a", default) or heatmap ("h") will be plotted.

Value

Returns NULL for avareange plot and cluster report data.frame for hetamap - see plotHeatmap for details.

Methods (by class)

• x = PlotSetPair,y = ANY: Method plot for signature 'PlotSetPair'

• x = PlotSetList,y = ANY: Method plot for signature 'PlotSetList'

• x = PlotSetArray,y = ANY: Method plot for signature 'PlotSetPair'

See Also

getPlotSetArray

Other plotting functions: getPlotSetArray, plotAverage, plotHeatmap

Examples

#load precalculated PlotSetArrays "plotset1" and "plotset2", usually these 
#objects are the output of getPlotSetArray function
load(system.file("extdata", "precalc_plotset.Rdata", package="seqplots"))

#plot with default values
plot(plotset2) #Average plot
plot(plotset2[1,], what='h') #Heatmap

#setting plot options
plot(plotset2, main='Title', xlab='Relative position [bp]', ylab='Signal', 
     colvec=rainbow(6, 0.7, 0.5), labels=LETTERS, legend_ext=TRUE, 
     legend_ext_pos='topright', legend_pos='topleft', ln.h=9)
     
plot(plotset2[2,], what='h', main="The heatmap", labels=LETTERS,
     ord = c(3,1,2), sortrows = TRUE, clusters = 2, clstmethod = "hclust", 
     cex.main = 20, cex.lab = 12, cex.legend = 12, xlab = "Rel. pos. [bp]", 
     ylab = "Signal", autoscale = FALSE, zmin = 0, zmax = 20, 
     clspace = rev(rainbow(4, 0.7, 0.5)) )

seqplots documentation built on Nov. 8, 2020, 4:52 p.m.