bioconductor-seqlogo

name	bioconductor-seqlogo
description	seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).
when_to_use	Use when: 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.. Not for: 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 D
user-invocable	false

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

• Homepage: https://bioconductor.org/packages/seqLogo
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/seqLogo/inst/doc/seqLogo.pdf

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