R/quickBar.R

In Krutik6/TimiRGeN: Time sensitive microRNA-mRNA integration, analysis and network generation tool

#' @title quickBar
#' @description Creates a bar plot which compares the confidence levels for
#' each wikipathway association to the filtered input data. The number of genes
#' in common between a pathway and the input data are taken into account to
#' generate confidence scores. This function is used specifically for a single
#' time point at a time, or if using "s" analysis, the function is used for a
#' single time point within a single gene type (miR or mRNA).
#' @param X Dataframes within a list including count information, confidence
#' scores and wikipathway information. This is the output from the enrichWiki
#' function. It will be stored as metadata within the MAE used in the enrichWiki
#' function. Data can be retrieved using [[i]][[j]] on the output of enrichWiki.
#' @param Y String which is associated to the nested dataframe selected for X.
#' This is the output from the enrichWiki function. It will be stored as
#' metadata within the MAE used in the enrichWiki function. Data can
#' be retrieved using names([[i]][j]) on the output of enrichWiki.
#' @param N Integer representing number of pathways to display. Default is 15.
#' @return Bar plot showing which pathways are most enriched for genes found
#' at each time point ("c") or at each time point within a gentype ("s").
#' @export
#' @importFrom ggplot2 ggplot aes geom_bar scale_fill_continuous labs theme
#' @importFrom ggplot2 unit element_rect
#' @importFrom ggplot2 element_text ggtitle coord_flip
#' @importFrom stats reorder p.adjust
#' @usage quickBar(X, Y, N)
#' @examples
#' library(org.Mm.eg.db)
#'
#' MAE <- MultiAssayExperiment()
#'
#' metadata(MAE)[["e_list"]] <- e_list_mouse
#'
#' MAE <- dloadGmt(MAE, species = "Mus musculus")
#'
#' MAE <- enrichWiki(MAE = MAE, method = 'c', ID_list = metadata(MAE)[[1]],
#'                    orgDB = org.Mm.eg.db, path_gene = assay(MAE, 1),
#'                    path_name = assay(MAE, 2), ID = "ENTREZID",
#'                    universe = assay(MAE, 1)[[2]])
#'
#' q <- quickBar(X = metadata(MAE)[[2]][[1]], Y = names(metadata(MAE)[[2]][1]))
#'
#' # to view bar plot enter plot(q)
quickBar <- function(X, Y, N=15){

    if (missing(X)) stop('X is missing. Input nested dataframe which is output from enrichWiki. Should be in the metadata of the MAE used in the enrichWiki function, and this can be retrieved using metadata(MAE)[[i]][[j]].')

    if (missing(Y)) stop('Y is missing. Input name of the nested dataframe associated with X. User can add any character.')

  Description <- Count <- NULL

    ggplot2::ggplot(head(X[which(X$p.adjust < 0.05),],n = N),
                    aes(x=reorder(Description, -p.adjust),
                        y=Count,
                        fill=-p.adjust)) +

      geom_bar(stat = "identity",
               width = 0.5) +

      scale_fill_continuous(type = "gradient") +

      labs(y = "Associated genes",
           x = "Wikipathways",
           fill = "p.adjust") +

      ggtitle(Y) +

      theme(plot.title = element_text(size=30, face = "bold", hjust = 0.5),
            legend.key.size = unit(5, "line"),
            legend.text=element_text(size=15),
            legend.title =element_text(size=15),
            axis.text=element_text(size=25),
            axis.title = element_text(size = 20))+

      theme(panel.background = element_rect(fill = 'white',
                                            colour = 'black'))+
      coord_flip()
}