plot_sequence_heatmap {memes} | R Documentation

## Visualize a heatmap of aligned sequences

### Description

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.

### Usage

    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)

    # Use different titles for list input
    plot_sequence_heatmap(sequences, title = c("A", "B"))

[Package memes version 1.0.4 Index]