Wrong results surrounding commented lines

[SPan-18]

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[SPan-18]

I am using the function formatR::tidy_dir() function on the following script. I have commented out some lines using the keyboard shortcut cmd+shift+C in the RStudio editor. Hence the placement of # in the script are automatic suggestions by the RStudio editor.

#' Make a surface plot
#'
#' @param tab a data-frame containing spatial co-ordinates and the variable to plot
#' @param coords_name name of the two columns that contains the co-ordinates of the points
#' @param var_name name of the column containing the variable to be plotted
#' @param h integer; controls smoothness of the spatial interpolation as appearing in the \code{mba.surf} function of the \code{MBA} package. Default is 8.
#' @param col.pal Optional; color palette, preferably divergent, use \code{colorRampPalette} function from \code{grDevices}. Deafult is 'RdYlBu'.
#' @param mark_points Logical; if \code{TRUE}, the input points are marked
#' @export
#' @importFrom MBA mba.surf
#' @importFrom ggplot2 ggplot aes_string geom_raster scale_fill_distiller geom_point scale_fill_gradientn
#' @importFrom ggplot2 theme_bw theme element_line element_blank element_text
#' @importFrom stats na.omit
surfaceplot <- function(tab, coords_name, var_name,
                        h = 8, col.pal = NULL,
                        mark_points = FALSE){

  surf <- mba.surf(tab[,c(coords_name, var_name)],
                   no.X = 250, no.Y = 250, h = h, m = 1, n = 1,
                   extend=FALSE)$xyz.est

  surf_df <- data.frame(expand.grid(surf$x, surf$y), z = as.vector(surf$z))
  surf_df <- na.omit(surf_df)
  names(surf_df) <- c("x", "y", "z")

  plot <- ggplot(surf_df, aes_string(x = 'x', y = 'y')) +
    geom_raster(aes_string(fill = 'z')) +
    # scale_fill_gradientn(colours = col.br(100)) +
    # scale_fill_gradientn(colours = col.RdBu(100)) +
    theme_bw() +
    theme(axis.ticks = element_line(linewidth = 0.25),
          panel.background = element_blank(),
          panel.grid = element_blank(),
          legend.box.just = "center",
          aspect.ratio = 1)

  if(is.null(col.pal)){
    plot <- plot + scale_fill_distiller(palette = "RdYlBu", direction = -1,
                                        label = function(x) sprintf("%.1f", x))
  }else{
    plot <- plot + scale_fill_gradientn(colours = col.pal)
  }

  if(mark_points){
    plot <- plot + geom_point(aes_string(x = coords_name[1], y = coords_name[2]), data = tab,
                              color = "black", fill = NA, shape = 21, stroke = 0.5, alpha = 0.5)
  }

  plot
}

The output, as given below, is obviously incorrect. The function runs without any error.

#' Make a surface plot
#'
#' @param tab a data-frame containing spatial co-ordinates and the variable to plot
#' @param coords_name name of the two columns that contains the co-ordinates of the points
#' @param var_name name of the column containing the variable to be plotted
#' @param h integer; controls smoothness of the spatial interpolation as appearing in the \code{mba.surf} function of the \code{MBA} package. Default is 8.
#' @param col.pal Optional; color palette, preferably divergent, use \code{colorRampPalette} function from \code{grDevices}. Deafult is 'RdYlBu'.
#' @param mark_points Logical; if \code{TRUE}, the input points are marked
#' @export
#' @importFrom MBA mba.surf
#' @importFrom ggplot2 ggplot aes_string geom_raster scale_fill_distiller geom_point scale_fill_gradientn
#' @importFrom ggplot2 theme_bw theme element_line element_blank element_text
#' @importFrom stats na.omit
surfaceplot <- function(tab, coords_name, var_name, h = 8, col.pal = NULL, mark_points = FALSE) {

    surf <- mba.surf(tab[, c(coords_name, var_name)], no.X = 250, no.Y = 250, h = h, m = 1, n = 1, extend = FALSE)$xyz.est

    surf_df <- data.frame(expand.grid(surf$x, surf$y), z = as.vector(surf$z))
    surf_df <- na.omit(surf_df)
    names(surf_df) <- c("x", "y", "z")

    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + plot
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + <-
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + ggplot(surf_df,
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + aes_string(x
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + =
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + "x",
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + y
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + =
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + "y"))
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + +
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + geom_raster(aes_string(fill
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + =
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + "z"))
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + +
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + #
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + scale_fill_gradientn(colours
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + =
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + col.br(100))
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + +
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + scale_fill_gradientn(colours
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + =
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + col.RdBu(100))
    plot <- ggplot(surf_df, aes_string(x = "x", y = "y")) + geom_raster(aes_string(fill = "z")) + # scale_fill_gradientn(colours = col.br(100)) +  scale_fill_gradientn(colours = col.RdBu(100)) + +
    theme_bw() + theme(axis.ticks = element_line(linewidth = 0.25), panel.background = element_blank(), panel.grid = element_blank(),
        legend.box.just = "center", aspect.ratio = 1)

    if (is.null(col.pal)) {
        plot <- plot + scale_fill_distiller(palette = "RdYlBu", direction = -1, label = function(x) sprintf("%.1f", x))
    } else {
        plot <- plot + scale_fill_gradientn(colours = col.pal)
    }

    if (mark_points) {
        plot <- plot + geom_point(aes_string(x = coords_name[1], y = coords_name[2]), data = tab, color = "black", fill = NA, shape = 21,
            stroke = 0.5, alpha = 0.5)
    }

    plot
}

My session information is as follows.

R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.5, RStudio 2024.4.2.764

Locale: en_US.UTF-8 / en_US.UTF-8 / en_US.UTF-8 / C / en_US.UTF-8 / en_US.UTF-8

Package version:
  formatR_1.14

[yihui]

https://yihui.org/formatr/#6-further-notes

[SPan-18]

Thanks Yihui for the clarification. As it turns out, special care needs to be taken while commenting out multiple lines of code especially for piping functions. The link above explains the rule. Hence, I am closing the issue.

[yihui]

I should really throw an error or at least emit a warning in this case.