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bioconductor-seqlogo

seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).

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bioMate-AI/biomate-bioconductor-kb
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seqLogo

When to Use

  • Visualizing sequence logos for DNA sequence alignments using seqLogo().
  • Representing position weight matrices (PWM) and their information content profiles using makePWM().
  • Plotting RNA sequence logos by specifying the RNA alphabet and custom fill colors.

When NOT to Use

  • For highly customized ggplot2-based sequence logos, use ggseqlogo instead because seqLogo uses the base grid package for rendering.
  • For protein/amino acid sequence logos, use ggseqlogo instead because seqLogo is currently implemented primarily for DNA/RNA sequences.

Data Requirements

  • A simple matrix or data.frame where column probabilities add up to 1.0.
  • An instance of the pwm class created by makePWM().

Key Parameters

  • pwm: The position weight matrix for which the sequence logo is to be plotted (can be a pwm object, matrix, or data.frame).
  • ic.scale: Logical indicating whether the height of each column is to be proportional to its information content.
  • fill: A named character vector to change the default colors for the nucleotides (e.g., A, C, G, T or U).
  • alphabet: Character string to specify the alphabet, such as "RNA" for RNA logos.

Best Practices

  • Construct a pwm object from a matrix or data frame using makePWM() to automatically check that column probabilities sum to 1.0.
  • Use ic.scale=FALSE if you want all columns to have the same uniform height rather than being scaled by information content.
  • When plotting RNA logos, specify alphabet="RNA" in makePWM() and provide fill colors for either c("A", "C", "G", "U") or c("A", "C", "G", "T").

Common Pitfalls

  • Unnormalized Matrix: Column probabilities do not sum to 1.0. Fix: Ensure the input matrix or data.frame is properly normalized before passing it to makePWM().
  • Incorrect color mapping for RNA logos: The default colors may not map correctly to Uracil. Fix: Provide a named character vector to the fill argument in seqLogo() with specific colors for A, C, G, and T/U.
  • Attempting to plot amino acid sequences: The package will fail or produce incorrect logos. Fix: Use a different package, as the vignette notes seqLogo is designed for DNA/RNA alignments.

Alternatives

  • ggseqlogo: Uses ggplot2 for rendering, allowing for more modern and flexible plot customization.
  • universalmotif: Provides comprehensive motif manipulation and visualization for various alphabets.
  • motifStack: Allows plotting stacked logos and tree-structured logos for multiple motifs.

Citations

  • Schneider, Thomas D., and R.Michael Stephens. 1990. "Sequence logos: a new way to display consensus sequences." Nucleic Acids Research 18 (20): 6097-6100.
  • Schneider, Thomas D., Gary D. Stormo, Larry Gold, and Andrzej Ehrenfeucht. 1986. "Information Content of Binding Sites on Nucleotide Sequences." Journal of Molecular Biology 188 (3): 415-31.

References

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