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Plot Sequence Logos with Difference Column

Source: R/seqLogoDiff.R
plot_seqlogo_with_diff.Rd

Creates a 3-column sequence logo plot showing upregulated sites, downregulated sites, and their difference (Up - Down) for each contrast. The difference column uses an independent y-axis scale appropriate for showing positive and negative frequency differences.

Usage

plot_seqlogo_with_diff(sig_sites)

Arguments

sig_sites

A data frame containing significant phosphorylation sites with required columns: contrast, regulation, and SequenceWindow.

Value

A patchwork object combining sequence logos with 3 columns per contrast row: upregulated, downregulated, and difference logos. Returns NULL if no contrasts have both upregulated and downregulated sequences.

Details

For each contrast, three sequence logos are displayed:

  • Upregulated: Amino acid frequencies at sites with increased phosphorylation (y-axis: 0-1)

  • Downregulated: Amino acid frequencies at sites with decreased phosphorylation (y-axis: 0-1)

  • Difference: The difference in frequencies (Up - Down), where positive values indicate enrichment in upregulated sites (y-axis: symmetric around 0)

See also

plot_diff_logo for difference logos only

Examples

# Create example data with phosphorylation site motifs
sig_sites <- data.frame(
  contrast = rep("KO_vs_WT", 20),
  regulation = rep(c("upregulated", "downregulated"), each = 10),
  SequenceWindow = c(
    # Upregulated: Proline-directed (CDK-like: S/T-P-x-K)
    "AAATPASPLTPGKRA", "GGGKSPVSPLTPGKR", "AAATPASPLTPGKRA",
    "LLLSQVSPKTPAAAA", "AAATPASPLTPGKRA", "GGGKSPVSPLTPGKR",
    "VVKTPASPLTPGKRA", "AAATPASPLTPGKRA", "LLLSQVSPKTPAAAA",
    "GGGKSPVSPLTPGKR",

    # Downregulated: Basophilic (PKA-like: R-R-x-S)
    "LRRRRSLAAAGKPAA", "GGRRRASVAAAGKPA", "LRRRRSLAAAGKPAA",
    "GKRRRSSLAAAGKPA", "LRRRRSLAAAGKPAA", "GGRRRASVAAAGKPA",
    "DKRRRSSLAAAGKPA", "LRRRRSLAAAGKPAA", "GKRRRSSLAAAGKPA",
    "GGRRRASVAAAGKPA"
  )
)

# Generate 3-column layout: Up, Down, Difference
p <- plot_seqlogo_with_diff(sig_sites)
print(p)