R/density.R

In Alanocallaghan/plotlytalk: Some utility functions for plotly

#' Density plot using plotly
#'
#' Creates a density plot of all columns of a matrix or data.frame like
#' structure.
#'
#' @param mat Matrix for column-wise kernel density estimate curves.
#' @param title Plot title.
#' @param xlab X axis label.
#' @param palette Colour palette function
#' (function that returns valid colour values, eg `rainbow`).
#'
#' @return A plotly htmlwidget
#'
#' @examples
#' plotly_density(iris[, -5],
#'    title = "Density plot of Iris dataset",
#'    xlab = "Value")
#' mat <- matrix(rnorm(10000), ncol = 10)
#' plotly_density(mat)
#' @importFrom magrittr %>%
#' @importFrom plotly plot_ly layout config
#' @export
plotly_density <- function(
        mat,
        title = "",
        xlab = "",
        palette = viridis
    ) {

    mat <- as.data.frame(mat)

    if (is.null(colnames(mat))) {
        colnames(mat) <- seq_len(ncol(mat))
    }
    densities <- lapply(seq_len(ncol(mat)), function(i) {
        stats::density(mat[, i, drop = TRUE])
    })

    coords <- lapply(
        seq_len(ncol(mat)),
        function(i) {
            data.frame(
                Sample = colnames(mat)[i],
                x = densities[[i]][["x"]],
                y = densities[[i]][["y"]]
            )
        }
    )

    plot_ly(
        do.call(rbind, coords),
        x = ~x,
        y = ~y,
        color = ~Sample,
        text = ~paste0(
          "Sample: ", Sample, "<br>",
          "x: ", x, "<br>",
          "Density: ", y
        ),
        hoverinfo = "text",
        colors = palette(ncol(mat)),
        type = "scatter",
        mode = "lines"
    ) %>% layout(
        title = title,
        hovermode = "closest",
        xaxis = list(title = xlab),
        yaxis = list(title = "Density")
    )
}