| 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
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