Plot motif-enrichment for individual experiments

Visualises the result from get_df_enrichment for a single motif by producing a plotly bar plot with the motif enrichment comparisons for one comparison dataset pair.

Usage

plot_enrichment_individual(
  result,
  enrichment_df,
  comparison_i,
  motif_i,
  label_colours,
  reference_index = 1,
  html_tags = TRUE
)

Arguments

result

A list with the following elements:

peaks: A list of peak files generated using read_peak_file.
alignments: A list of alignment files.
exp_type: A character vector of experiment types.
exp_labels: A character vector of experiment labels.
read_count: A numeric vector of read counts.
peak_count: A numeric vector of peak counts.

enrichment_df

A data frame containing the motif enrichment results, produced using get_df_enrichment.

comparison_i

The index of the comparison dataset to plot.

motif_i

The index of the motif to plot.

label_colours

A vector with colours (valid names or hex codes) to use for "No" and "Yes" bar segments.

reference_index

An integer specifying the index of the peak file to use as the reference dataset for comparison. Indexing starts from 1. (default = 1)

html_tags

Logical. If TRUE, returns the plot as a tagList object.

Value

A plotly object with the peak motif enrichment data. If html_tags is TRUE, the function returns a tagList object instead.

Examples

data("CTCF_ChIP_peaks", package = "MotifPeeker")
data("CTCF_TIP_peaks", package = "MotifPeeker")
data("motif_MA1102.3", package = "MotifPeeker")
data("motif_MA1930.2", package = "MotifPeeker")
input <- list(
    peaks = list(CTCF_ChIP_peaks, CTCF_TIP_peaks),
    exp_type = c("ChIP", "TIP"),
    exp_labels = c("CTCF_ChIP", "CTCF_TIP"),
    read_count = c(150, 200),
    peak_count = c(100, 120)
)
segregated_input <- segregate_seqs(input$peaks[[1]], input$peaks[[2]])
motifs <- list(
    motifs = list(motif_MA1930.2, motif_MA1102.3),
    motif_labels = list("MA1930.2", "MA1102.3")
)
    
# \donttest{
    if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38")) {
        genome_build <-
            BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
        enrichment_df <- get_df_enrichment(
            input, segregated_input, motifs, genome_build, reference_index = 1,
            workers = 1
        )
        label_colours <- c("red", "cyan")
    
        plt <- plot_enrichment_individual(
            input, enrichment_df, comparison_i = 2, motif_i = 1,
            label_colours = label_colours, reference_index = 1, html_tags = FALSE
        )
        print(plt)
    }
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# }

Usage

Arguments

Value

See also

Examples