plotPatternDensityMap: Plot heatmaps for several patterns in DNA sequence

Description Usage Arguments Value Methods (by class) See Also Examples

Description

Plot heatmaps for several patterns in DNA sequence

Usage

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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)

See Also

PatternHeatmap plotHeatmapList smoothHeatmap

Examples

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mgperry/heatmaps documentation built on May 22, 2019, 8:53 p.m.