plotPatternDensityMap: Plot heatmaps for several patterns in DNA sequence

In mgperry/heatmaps: Flexible Heatmaps for Functional Genomics and Sequence Features

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))

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