R/plot_bar.R

In omu: A Metabolomics Analysis Tool for Intuitive Figures and Convenient Metadata Collection

#' Create a bar plot
#' @description Creates a ggplot2 object using the output file from the count_fold_changes function
#' @param fc_data The output file from Count_Fold_Changes
#' @param fill A character vector of length 2 containing colors for filling the bars,
#' the first color is for the "Decrease" bar while the second
#' is for "Increase"
#' @param outline_color A character vector of length 2 containing colors for the bar outlines
#' @param size A numeric vector of 2 numbers for the size of the bar outlines.
#' @importFrom ggplot2 ggplot
#' @importFrom ggplot2 aes
#' @importFrom ggplot2 geom_bar
#' @importFrom ggplot2 theme
#' @importFrom ggplot2 theme_bw
#' @importFrom ggplot2 element_text
#' @importFrom ggplot2 element_blank
#' @importFrom ggplot2 element_line
#' @importFrom ggplot2 scale_fill_manual
#' @importFrom ggplot2 scale_size_manual
#' @importFrom ggplot2 scale_color_manual
#' @examples
#' c57_nos2KO_mouse_countDF <- assign_hierarchy(c57_nos2KO_mouse_countDF, TRUE, "KEGG")
#' \dontshow{c57_nos2KO_mouse_countDF <- c57_nos2KO_mouse_countDF[1:20,]}
#' t_test_df <- omu_summary(count_data = c57_nos2KO_mouse_countDF,
#' metadata = c57_nos2KO_mouse_metadata, numerator = "Strep", denominator = "Mock",
#' response_variable = "Metabolite", Factor = "Treatment",
#' log_transform = TRUE, p_adjust = "BH", test_type = "welch")
#'
#' fold_change_counts <- count_fold_changes(count_data = t_test_df,
#' column = "Class", sig_threshold = 0.05, keep_unknowns = FALSE)
#'
#' plot_bar(fc_data = fold_change_counts, fill = c("firebrick2", "dodgerblue2"),
#' outline_color = c("black", "black"), size = c(1,1))
#' @export

plot_bar <- function(fc_data, fill, size = c(1,1), outline_color = c("black", "black")){
 Class <- Significant_Changes <- color <- NULL

if(any(names(fc_data) %in% "Significant_Changes")==FALSE){

  stop("fc_changes needs to be a dataframe from the count_fold_changes function")

}

if(isTRUE(length(fill) == 2)==FALSE | isTRUE(is.character(fill))==FALSE){

  stop("fill must be a character vector of length 2 containing two valid color names")

}

colnames(fc_data)[1] <- "Class"
    ggplot(data = fc_data, aes(x=reorder(Class, -Significant_Changes), y = Significant_Changes)) +
           geom_bar(stat = "identity", aes(fill = color, color = color, size = color)) +
           theme_bw() +
           theme(axis.text.x = element_text(angle = 30, hjust=1, vjust=1, size = 10),
           axis.text.y = element_text(size = 10)) +
           theme(panel.border = element_blank(), axis.line = element_line(color = "Black", size=1,
           lineend = "square")) +
           theme(plot.title = element_text(hjust = 0.5)) +
           scale_size_manual(values = size) +
           scale_fill_manual(values = fill) +
           scale_color_manual(values = outline_color)
}