R/plotLONGO.r

In BioHPC/LONGO: Long gene expression as a metric for neuronal identity

#' Plot function
#'
#' This is a internal function. This function allows the program to
#' plot the data.
#'
#' @param simp.df dataframe to be plotted
#' @return Returns nothing
plotLONGO <- function(simp.df) {
    x_vals <- (simp.df$kb_length)
    ymax <- (max(simp.df[, 2:(ncol(simp.df))]) * 1.2)
    yminim <- min(simp.df[, 2:(ncol(simp.df))])
    png(
        "LONGO_out.png",
        width = 6,
        height = 6,
        units = "in",
        res = 300
    )
    matplot(
        x = x_vals,
        y = simp.df[, 2],
        type = "l",
        col = 1,
        xlab = "Gene length (kb)",
        ylab = "Gene expression",
        ylim = c(yminim, ymax),
        main = "LONGO output"
    )
    for (i in 3:ncol(simp.df)) {
        par(new = TRUE)
        matplot(
            x = x_vals,
            y = simp.df[, i],
            type = "l",
            col = i - 1,
            xlab = "",
            ylab = "",
            ylim = c(yminim, ymax),
            axes = FALSE
        )
    }
    labels <- colnames(simp.df)
    legend(
        "topright",
        legend = c(labels[2:length(labels)]),
        col = 2:ncol(simp.df) - 1,
        lty = 1,
        cex = 0.8,
        ncol = 2
    )
    dev.off()
}