R/plot_genomic_annotations.R

In ALPS: AnaLysis routines for ePigenomicS data

#' Plot genomic annotations
#'
#' @description plot the annotations of genomic regions
#' either as \code{stacked bar} or \code{heatmap}.
#' The function takes the output of \code{\link{get_genomic_annotations}}
#' directly or it is also compatible with a similar data.frame.
#'
#' @param annotations_df a data.frame of genomic annotations.
#' It can either be of one sample or of multiple samples as a data.frame
#' @param plot_type either \code{bar} plot or \code{heatmap},
#' default \code{bar}
#' @param col vector of colors for each feature in \code{annotations_df}.
#' If provided these colors are used, if not a custom set of distinct
#' colors will be used. Default \code{NULL}
#'
#' @importFrom reshape2 melt
#' @importFrom utils head
#'
#' @return \code{ggplot2} plot
#'
#' @export
#'
#' @examples
#'
#' ## load example data
#'
#' chr21_data_table <- system.file('extdata/bw', 'ALPS_example_datatable.txt', package = 'ALPS', mustWork = TRUE)
#'
#' ## attach path to bw_path and bed_path
#' d_path <- dirname(chr21_data_table)
#'
#' chr21_data_table <- read.delim(chr21_data_table, header = TRUE)
#' chr21_data_table$bw_path <- paste0(d_path, '/', chr21_data_table$bw_path)
#' chr21_data_table$bed_path <- paste0(d_path, '/', chr21_data_table$bed_path)
#'
#' g_annotations <- get_genomic_annotations(data_table = chr21_data_table,
#' merge_level = 'group_level')
#'
#' plot_genomic_annotations(annotations_df = g_annotations, plot_type = 'heatmap')

plot_genomic_annotations <- function(annotations_df, plot_type = "bar", col = NULL) {

    assertthat::assert_that(is.data.frame(annotations_df), msg = "Please provide `annotations_df`")

    ## colors
    if (!is.null(col)) {

        col_pal <- col
    } else {

        dist_cols <- c("#e6194B", "#3cb44b",
            "#ffe119", "#4363d8", "#f58231",
            "#911eb4", "#42d4f4", "#f032e6",
            "#bfef45", "#fabebe", "#469990",
            "#e6beff", "#9A6324", "#fffac8",
            "#800000", "#aaffc3", "#808000",
            "#ffd8b1", "#000075", "#a9a9a9",
            "#ffffff", "#000000")

        feature_names <- annotations_df$Feature %>%
          as.character() %>% unique

        num_features <- feature_names %>% length

        col_pal <- dist_cols %>% utils::head(n = num_features)
        names(col_pal) <- feature_names
    }

    ## single barplot
    if (ncol(annotations_df) == 2) {

        message("  `annotation_df` has only 2 columns, plotting a barplot")

        annotations_stack <- annotations_df %>%
            dplyr::mutate(group = "group")

        plt <- ggplot(annotations_stack, aes(x = group, y = Frequency, fill = Feature)) +
          geom_bar(stat = "identity") +
          scale_fill_manual(values = col_pal) +
          theme_classic(base_size = 14) +
          scale_y_continuous(limits = c(0, 100), expand = c(0, 0)) +
          theme(axis.title.x = element_blank(),
                axis.text = element_text(color = "black"),
                axis.text.x = element_blank(),
                axis.ticks.length = unit(0.25,"cm"),
                axis.ticks.x = element_blank(),
                axis.line.x = element_blank()) +
          ylab("% of peaks in feature")

    } else {

        ## if > 1 samples in annotations_df
        suppressMessages(annotations_mlt <- annotations_df %>%
            reshape2::melt())

        if (plot_type == "bar") {

            plt <- ggplot(annotations_mlt, aes(x = variable, y = value, fill = Feature)) +
              geom_bar(stat = "identity") +
              scale_fill_manual(values = col_pal) +
              theme_classic(base_size = 14) +
              scale_y_continuous(limits = c(0, 100), expand = c(0, 0)) +
              theme(axis.title.x = element_blank(),
                    axis.text = element_text(color = "black"),
                    axis.ticks.length = unit(0.25, "cm"),
                    axis.ticks.x = element_blank(),
                    axis.line.x = element_blank()) +
                ylab("% of peaks in feature")


        } else {
            ## heatmap
            plt <- ggplot(annotations_mlt, aes(x = variable, y = Feature, fill = value)) +
              geom_tile(size = 0.65, color = "white") +
              theme_minimal(base_size = 14) +
              theme(axis.ticks = element_blank()) +
              scale_fill_viridis_c(name = "% of peaks") +
              theme(axis.text = element_text(color = "black"),
                    panel.grid = element_blank()) +
                xlab("")
        }
    }

    return(plt)
}