Plot diagnostics of binned sequences — plotBinDiagnostics • monaLisa

Plot various diagnostics of binned sequences. Three plot types are available:

length: plots the distribution of sequence lengths within each bin.
GCfrac: plots the distribution of GC fractions within each bin.
dinucfreq: plots a heatmap of the relative frequency of each dinucleotide, averaged across the sequences within each bin. The values are centered for each dinucleotide to better highlight differences between the bins. The average relative frequency of each dinucleotide (across the bins) is indicated as well.

Usage

plotBinDiagnostics(
  seqs,
  bins,
  aspect = c("length", "GCfrac", "dinucfreq"),
  draw_quantiles = c(0.25, 0.5, 0.75),
  ...
)

Arguments

seqs: DNAStringSet object with sequences.
bins: Factor of the same length and order as seqs, indicating the bin for each sequence. Typically the return value of bin.
aspect: The diagnostic to plot. Should be one of "length", "GCfrac" and "dinucfreq", to plot the distribution of sequence lengths, the distribution of GC fractions and the average relative dinucleotide frequencies across the bins.
draw_quantiles: For aspect="length" or "GCfrac", draw vertical lines at the given quantiles of the density estimate. If NULL, no quantile lines will be drawn.
...: Additional argument passed to getColsByBin.

Value

For aspect="length" or "GCfrac", returns a ggplot object. For aspect="dinucfreq", returns (invisibly) a Heatmap-class object.

Examples

seqs <- Biostrings::DNAStringSet(
  vapply(1:250, function(i) paste(sample(x = c("A", "C", "G", "T"),
                                         size = round(stats::rnorm(1, 20, 5)),
                                         replace = TRUE), collapse = ""), "")
)
bins <- factor(rep(c("a", "b", "c", "d", "e"), each = 50))
plotBinDiagnostics(seqs, bins, aspect = "length")

plotBinDiagnostics(seqs, bins, aspect = "GCfrac", draw_quantiles = NULL)

plotBinDiagnostics(seqs, bins, aspect = "dinucfreq")