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.
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 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`.
whether to include a sequence logo above the heatmap
alphabet colorscheme to use. One of: DNA, RNA, AA.
value from 0 to 1 determining the horizontal justification of the title. Default: 0.
ratio of logo:heatmap heights. Given as: c(logo_height, heatmap_height). Values are not absolute. Ignored when logo = FALSE.
passed to ggplot2::theme(legend.position). Default: "none". Values can be: "none", "left", "right", "top", "bottom", or coordinates in c(x,y) format.
a ggplot object of the sequence heatmap ranked by the order of sequences
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` #>