#' Function to Filter Differentially Expressed Genes (DEGs)

#'

#' This function filters out genes based on their expression change status.

#' It returns the names of genes which are not "stable".

#'

#' @param df A data frame containing gene expression data.

#' @return A vector of gene names that are differentially expressed.

#' @examples

#' DEG_deseq2_file <- system.file("extdata", "DEG_deseq2.rds", package = "TransProR")

#' DEG_deseq2 <- readRDS(DEG_deseq2_file)

#' DEG_deseq2_test <- deg_filter(DEG_deseq2)

#' @export

deg_filter <- function(df){

  # Selecting gene names where change is not "stable"

  rownames(df)[df$change != "stable"]

}

#' Function to Create a Venn Diagram of DEGs

#'

#' This function creates a Venn Diagram using the ggVennDiagram package.

#' It allows customization of various aesthetic elements of the diagram.

#' @importFrom ggplot2 alpha scale_fill_gradient scale_color_manual scale_x_continuous expansion

#' @importFrom ggVennDiagram ggVennDiagram

#' @param degs_list A list of DEG sets for Venn Diagram creation.

#' @return A ggplot object representing the Venn Diagram.

#' @examples

#' data("all_degs_venn", package = "TransProR")

#' four_degs_venn <- four_degs_venn(all_degs_venn)

#' @export

four_degs_venn <- function(degs_list){

  # Defining edge colors and alpha transparency for the Venn Diagram

  edge_colors <- c(ggplot2::alpha("#1b64bb", 0.5), ggplot2::alpha("#13828e", 0.5),

                   ggplot2::alpha("#337c3a", 0.5), ggplot2::alpha("#9e9d39", 0.5))

  edge_color <- ggplot2::alpha(c("#1b64bb","#13828e","#337c3a","#9e9d39"), 0.8)

  # Creating a Venn Diagram using 'ggVennDiagram'

  ggVennDiagram::ggVennDiagram(

    degs_list,

    set_size = 5,  # Font size for group names

    set_color = edge_color,  # Color for group names

    label_alpha= 0,  # Transparency of background box for labels

    label_size = 4,  # Font size for labels

    edge_size = 3   # Thickness of edges

  ) +

    ggplot2::scale_fill_gradient(low="#e1f2f1", high = "#11786b") +  # Gradient fill based on values

    ggplot2::scale_color_manual(values = edge_colors) +  # Manually set edge colors

    ggplot2::scale_x_continuous(expand = ggplot2::expansion(mult = .3))  # Adjusting x-axis scaling

}