plot {seqplots} | R Documentation

## Generic plot function for SeqPlots package calsses

### 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)) )

[Package seqplots version 1.25.0 Index]