R/plot_boxplot.R

In EmanuelSoda/ScreenR: Package to Perform High Throughput Biological Screening

#' @title Plot Barcodes Hit
#' @description This function plots a boxplot for each sample for the genes
#'              passed as input. It can be used to see the overall trend of a
#'              gene and so to visualize if the gene is up or down regulated.
#' @param screenR_Object The ScreenR object obtained using the
#'                       \code{\link{create_screenr_object}}
#' @param group_var The variable that as to be used to filter the data, for
#'                  example the different treatment
#' @param fill_var The variable used to fill the boxplot
#' @param alpha A value for the opacity of the plot.
#'              Allowed values are in the range 0 to 1
#' @param genes The vector of genes that will be displayed
#' @param nrow The number of rows in case multiple genes are plotted
#' @param ncol The number of columns in case multiple genes are plotted
#' @param type The type of plot to use "boxplot" or "violinplot"
#' @param scales The scales used for the facet.
#'               Possible values can be "free", "fixed" and "free_y"
#' @concept  plot
#' @importFrom dplyr sym
#' @importFrom ggplot2 geom_violin
#' @return A boxplot
#' @export
#' @examples
#' object <- get0("object", envir = asNamespace("ScreenR"))
#'
#' plot_boxplot(object,
#'     genes = c("Gene_34"),
#'     group_var = c("T1", "T2", "TRT"), nrow = 1, ncol = 2,
#'     fill_var = "Day", type = "violinplot"
#' )
#'
plot_boxplot <- function(screenR_Object, genes, group_var, alpha = 0.5,
    nrow = 1, ncol = 1, fill_var = "Sample",
    type = "boxplot", scales = "free") {
    data <- screenR_Object@data_table

    # Select only the hit gene
    data <- dplyr::filter(data, .data$Gene %in% genes)

    # Select only the sample of interest
    data <- dplyr::filter(data, .data$Treatment %in% group_var)

    plot <- ggplot2::ggplot(data, aes(.data$Sample, .data$Frequency,
        fill = !!sym(fill_var)
    ))
    if (type == "boxplot") {
        plot <- plot + geom_boxplot()
    } else if (type == "violinplot") {
        plot <- plot + geom_violin()
    } else {
        stop("The only available type of plot are boxplot and violinplot")
    }

    if (length(genes) > 1) {
        plot <- plot + facet_wrap("Gene",
            nrow = nrow,
            ncol = ncol, scales = scales
        )
    }

    return(plot)
}