R/granplot.R

In G2Sd: Grain-Size Statistics and Description of Sediment

granplot <-
  function(
    x,
    xc = 1,
    meshmin = 1,
    hist = TRUE,
    cum = TRUE,
    main = "",
    col.cum = "red",
    col.hist = "darkgray",
    cexname = 0.9,
    cexlab = 1.3,
    decreasing = FALSE,
    log.scale = TRUE
  ) {
    x <- x[order(as.numeric(row.names(x)), decreasing = decreasing), ]

    um <- as.numeric(row.names(x))
    # Remplacer les valeurs 0 et negatives pour eviter les problemes avec log10
    if (!is.na(pmatch(0, um))) {
      um[pmatch(0, um)] = meshmin
    }
    um[um <= 0] <- meshmin

    if (length(xc) == 1) {
      sum.sieve = sum(x[, xc])
      class.weight = (x[, xc] * 100) / sum.sieve
      class.weight.cum = round(cumsum(class.weight), 2)
      weight.gran <- data.frame(
        um = um,
        weight = class.weight,
        weight.cum = class.weight.cum
      )
      hist.cum.plot <- ggplot(weight.gran) +
        theme(
          panel.background = element_blank(),
          panel.grid = element_line(colour = "gray"),
          axis.title = element_text(size = 13, face = "bold"),
          axis.text = element_text(size = 11, colour = "black"),
          strip.text.x = element_text(size = rel(1.0), face = "bold"),
          axis.ticks = element_line(colour = "black"),
          axis.line = element_line(colour = "black")
        ) +
        labs(title = names(granulo)[xc])

      if (hist == TRUE & cum == TRUE) {
        if (log.scale) {
          if (decreasing) {
            hist.cum.plot <- hist.cum.plot +
              geom_bar(
                aes(x = um, y = weight),
                stat = "identity",
                fill = col.hist
              ) +
              geom_line(
                aes(x = um, y = weight.cum),
                colour = col.cum,
                linewidth = 1.5
              ) +
              ylab("Weight (%)") +
              xlab(expression(log[10](Particule ~ size))) +
              scale_y_continuous(
                sec.axis = sec_axis(~ . * 1, name = "Percentage cum.(%)")
              ) +
              scale_x_continuous(trans = .reverselog_trans(10))
          } else {
            hist.cum.plot <- hist.cum.plot +
              geom_bar(
                aes(x = um, y = weight),
                stat = "identity",
                fill = col.hist
              ) +
              geom_line(
                aes(x = um, y = weight.cum),
                colour = col.cum,
                linewidth = 1.5
              ) +
              ylab("Weight (%)") +
              xlab(expression(log[10](Particule ~ size))) +
              scale_y_continuous(
                sec.axis = sec_axis(~ . * 1, name = "Percentage cum.(%)")
              ) +
              suppressWarnings(scale_x_log10())
          }
        } else {
          hist.cum.plot <- hist.cum.plot +
            geom_bar(
              aes(x = um, y = weight),
              stat = "identity",
              fill = col.hist
            ) +
            geom_line(
              aes(x = um, y = weight.cum),
              colour = col.cum,
              linewidth = 1.5
            ) +
            ylab("Weight (%)") +
            xlab("Particule size") +
            scale_y_continuous(
              sec.axis = sec_axis(~ . * 1, name = "Percentage cum.(%)")
            )
        }

        print(hist.cum.plot)
      }
      if (hist == FALSE & cum == TRUE) {
        if (log.scale) {
          if (decreasing) {
            hist.cum.plot <- hist.cum.plot +
              geom_line(
                aes(x = um, y = weight.cum),
                colour = col.cum,
                linewidth = 1.5
              ) +
              ylab("Percentage cum.(%)") +
              xlab(expression(log[10](Particule ~ size))) +
              scale_x_continuous(trans = .reverselog_trans(10))
          } else {
            hist.cum.plot <- hist.cum.plot +
              geom_line(
                aes(x = um, y = weight.cum),
                colour = col.cum,
                linewidth = 1.5
              ) +
              ylab("Percentage cum.(%)") +
              xlab(expression(log[10](Particule ~ size))) +
              suppressWarnings(scale_x_log10())
          }
        } else {
          hist.cum.plot <- hist.cum.plot +
            geom_line(
              aes(x = um, y = weight.cum),
              colour = col.cum,
              linewidth = 1.5
            ) +
            ylab("Percentage cum.(%)") +
            xlab("Particule size")
        }

        print(hist.cum.plot)
      }

      if (hist == TRUE & cum == FALSE) {
        if (log.scale) {
          if (decreasing) {
            hist.cum.plot <- hist.cum.plot +
              geom_bar(
                aes(x = um, y = weight),
                stat = "identity",
                fill = col.hist
              ) +
              ylab("Weight (%)") +
              xlab(expression(log[10](Particule ~ size))) +
              scale_x_continuous(trans = .reverselog_trans(10))
          } else {
            hist.cum.plot <- hist.cum.plot +
              geom_bar(
                aes(x = um, y = weight),
                stat = "identity",
                fill = col.hist
              ) +
              ylab("Weight (%)") +
              xlab(expression(log[10](Particule ~ size))) +
              suppressWarnings(scale_x_log10())
          }
        } else {
          hist.cum.plot <- hist.cum.plot +
            geom_bar(
              aes(x = um, y = weight),
              stat = "identity",
              fill = col.hist
            ) +
            ylab("Weight (%)") +
            xlab("Particule size")
        }

        print(hist.cum.plot)
      }
    }

    if (length(xc) != 1) {
      class.weight = sapply(x[, xc], function(x) {
        (x / sum(x, na.rm = TRUE)) * 100
      })
      class.weight.cum = as.data.frame(round(apply(class.weight, 2, cumsum), 2))
      row.names(class.weight.cum) <- row.names(x)
      class.weight.cum <- class.weight.cum |>
        t() |>
        as.data.frame() |>
        rownames_to_column("var") |>
        pivot_longer(cols = -var, names_to = "gsize", values_to = "value")
      class.weight.cum$gsize <- as.numeric(class.weight.cum$gsize)

      p <- ggplot(
        class.weight.cum,
        aes(
          x = .data[["gsize"]],
          y = .data[["value"]],
          shape = .data[["var"]],
          col = .data[["var"]]
        )
      ) +
        geom_line(linewidth = 2) +
        theme_bw() +
        labs(
          x = if (log.scale) {
            expression(log[10](Particule ~ size))
          } else {
            "Particule size"
          },
          y = "Percentage cum.(%)",
          title = main
        ) +
        theme(
          plot.title = element_text(
            size = rel(1.5),
            colour = "black",
            face = "bold"
          ),
          axis.title.y = element_text(size = 13, face = "bold"),
          axis.title.x = element_text(size = 13, face = "bold"),
          axis.text.y = element_text(size = 11, face = "bold"),
          axis.text.x = element_text(size = 11, face = "bold")
        ) +
        scale_colour_hue("Stations")

      if (log.scale) {
        p <- p + suppressWarnings(scale_x_log10())
      }

      print(p)
    }
  }