R/covBars_buildMain.R

In GenVisR: Genomic Visualizations in R

#' Construct coverage cohort plot
#'
#' given a data frame construct a plot to display coverage as percentage bars
#' for a group of samples
#' @name covBars_buildMain
#' @param data_frame object of class data frame containing columns depth,
#' sample, bp
#' @param col vector of colors for the coverage bars
#' @param plot_title character string for title of plot
#' @param x_lab_size integer specifying the size of the X label
#' @param y_lab_size integer specifying the size of the Y label
#' @param facet_lab_size integer specifying the size of the faceted labels
#' @param layers Additional layers to be plotted, can be a theme but must be a
#' ggplot layer
#' @return ggplot object
#' @import ggplot2
#' @importFrom viridis scale_fill_viridis
#' @noRd

covBars_buildMain <- function(data_frame, col, plot_title=NULL, x_lab_size=12,
                              y_lab_size=12, facet_lab_size=10, layers=NULL)
{
    xmelt <- data_frame

    # Define Theme of plot
    theme <- theme(strip.text.y=element_text(angle=0, size=facet_lab_size),
                   axis.text.y=element_blank(),
                   axis.ticks.y=element_blank(),
                   panel.grid.major=element_blank(),
                   panel.grid.minor=element_blank(),
                   legend.position='right',
                   axis.title.x=element_text(size=x_lab_size, face='bold'),
                   axis.title.y=element_text(size=y_lab_size, face='bold'))

    # Define parameters of plot
    facet <- facet_grid(sample ~ ., scales='free', space='free')
    if(!is.null(col))
    {
        fill_gradient <- scale_fill_gradientn(colours=col)
    } else {
        fill_gradient <- viridis::scale_fill_viridis()
    }
    
    ylabel <- ylab('Sample')
    xlabel <- xlab('Cumulative Coverage')

    # Define main plot using boundaries and then plot actual data
    p1 <- ggplot(data=xmelt,
                 mapping=aes_string(xmin='xmin', xmax='bp',
                                    ymin=0, ymax=1)) + geom_rect(alpha=0) +
        scale_x_continuous(expand=c(0,0)) + scale_y_continuous(expand=c(0,0))
    
    p1 <- p1 + geom_rect(data=xmelt,
                         mapping=aes_string(xmin='xmin', xmax='bp',
                                            ymin=0, ymax=1, fill='depth'))

    # build the plot
    p1 <- p1 + fill_gradient + ylabel + xlabel + facet + theme

    # if there are other layers, add them
    if(!is.null(layers))
    {
        p1 <- p1 + layers
    }
    
    # if title is supplied plot it
    if(!is.null(plot_title))
    {
        p1 <- p1 + ggtitle(plot_title)
    }
    
    return(p1)
}