plot.graph.R

#' Plot graphs
#' @description Plot different charts.
#' @param data Input data e.g. data frame
#' @param type Type of graph e.g. ("boxplot", "violinplot", "jitterplot", "barplot")
#' @param x Values for x-axis, e.g. values of a column to be passed to aes(x = ...) of \link{ggplot2}
#' @param y Values for y-axis, values of a column to be passed to aes(y = ...) of \link{ggplot2}
#' @param geom_plot_args A list of rguments to \link{ggplot2}
#' @import ggplot2
#' @import data.table
#' @examples
#' brainCalculatedMetadata <- calculate.metadata(metadata, brainRows)
#' @return

plot.graph <- function(data, type = "jitter", x, y, geom_plot_args = list()) {
    #check if data is a data table
    if (!is.data.table(data)) data <- data.table(data)
    if(type == "boxplot") {
      ggplot(data, aes(x = data[[x]], y = data[[y]])) +
        do.call("geom_boxplot", geom_plot_args) +
        xlab(x) +
        ylab(y)
    }
    else if(type == "violinplot") {
      ggplot(data, aes(x = data[[x]], y = data[[y]])) +
        do.call("geom_violin", geom_plot_args) + 
        geom_jitter(size = 0.4, width = 0.15) +
        stat_summary(fun.data = summary.violin, color = "black") +
        xlab(x) +
        ylab(y)
    }
    else if(type == "jitter") {
      ggplot(data, aes(x = data[[x]], y = data[[y]])) +
        do.call("geom_jitter", geom_plot_args) +
        xlab(x) +
        ylab(y)
    }
   else if(type == "barplot") {
      ggplot(data, aes(x = data[[x]])) +
        do.call("geom_bar", geom_plot_args) +
        xlab(x) +
        ylab(y)
    }
}

#' Calculation of median + range
#' @param x Input from ggplot
summary.violin <- function(x) {
  mu <- mean(x)
  sigma1 <- mu-sd(x)
  sigma2 <- mu+sd(x)
  return(c(y=mu, ymin=sigma1, ymax=sigma2))
}