Visualize a heatmap of aligned sequences

Source: R/sequence_heatmap.R

Sometimes it is useful to visualize individual motif matches in aggregate to understand how sequence variability contributes to motif matches. This function creates a heatmap where each row represents a single sequence and each column represents a position. Cells are colored by the sequence at that position. Sequences are optionally aggregated into a sequence logo aligned in register with the heatmap to visualize how sequence variability contributes to motif makeup.

plot_sequence_heatmap(
  sequence,
  title = NULL,
  logo = TRUE,
  alph = c("DNA", "RNA", "AA"),
  title_hjust = 0,
  heights = c(1, 5),
  legend = "none"
)

Arguments

sequence

character vector of sequences, plot will be ranked in order of the sequences. Each sequence must be equal length. Alternately, sequence can be a named list in which case each plot will be titled by the names of the list entries.

title

title of the plot. Default: NULL. If sequence is a named list of sequences, title defaults to the list entry names. Set to NULL to override this behavior. To use a different title than the list entry name, pass a vector of names to `title`.

logo

whether to include a sequence logo above the heatmap

alph

alphabet colorscheme to use. One of: DNA, RNA, AA.

title_hjust

value from 0 to 1 determining the horizontal justification of the title. Default: 0.

heights

ratio of logo:heatmap heights. Given as: c(logo_height, heatmap_height). Values are not absolute. Ignored when logo = FALSE.

legend

passed to ggplot2::theme(legend.position). Default: "none". Values can be: "none", "left", "right", "top", "bottom", or coordinates in c(x,y) format.

Value

a ggplot object of the sequence heatmap ranked by the order of sequences

See also

runFimo

Examples

data(example_fimo, package = "memes")
genome <- BSgenome.Dmelanogaster.UCSC.dm3::BSgenome.Dmelanogaster.UCSC.dm3
motifs <- add_sequence(example_fimo, genome)
plot_sequence_heatmap(motifs$sequence)


# Use on named list
sequences <- list("set 1" = motifs$sequence[1:100], 
                  "set 2" = motifs$sequence[101:200])
plot_sequence_heatmap(sequences)
#> $`set 1`

#> 
#> $`set 2`

#> 

# Use different titles for list input
plot_sequence_heatmap(sequences, title = c("A", "B"))
#> $`set 1`

#> 
#> $`set 2`

#>