plotPatternDensityMap {heatmaps} | R Documentation

## Plot heatmaps for several patterns in DNA sequence

### Description

Plot heatmaps for several patterns in DNA sequence

### Usage

    plotPatternDensityMap(seq, patterns, ...)

    ## S4 method for signature 'DNAStringSet'
    plotPatternDensityMap(seq, patterns, coords = NULL,
      min.score = "80%", sigma = c(3, 3), output.size = NULL,
      options = NULL, ...)

### Arguments

`seq` | DNAStringSet of equal width
`patterns` | A vector or list of patterns
`...` | Additional Heatmap plotting options This function is a convenient wrapper for plotting many different patterns for the same set of sequences. PatternHeatmap() is applied to the sequence for each pattern in the list, they are passed to smoothHeatmap() with the supplied parameters and finally PlotHeatmapList(). If fine-grained control is desired, or you want to mix other plot types, then more information is available in the vignette.
`coords` | Heatmap coords
`min.score` | Minimum score for PWM match
`sigma` | Bandwith for smoothing kernel
`output.size` | Output size of final image
`options` | Heatmap plotting options

### Value

invisible(0)

### Methods (by class)

- `DNAStringSet`: Plot heatmaps for several patterns in DNA sequence

### See Also

PatternHeatmap plotHeatmapList smoothHeatmap

### Examples

    data(HeatmapExamples)
    plotPatternDensityMap(string_set, c("AT", "CG"), coords=c(-200, 200))

[Package heatmaps version 1.12.0 Index]