plotPatternDensityMap {heatmaps} | R Documentation |
Plot heatmaps for several patterns in DNA sequence
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, ...)
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 |
invisible(0)
DNAStringSet
: Plot heatmaps for several patterns in DNA sequence
PatternHeatmap plotHeatmapList smoothHeatmap
data(HeatmapExamples) plotPatternDensityMap(string_set, c("AT", "CG"), coords=c(-200, 200))