Adding a Dot to Filled Contour Plots: A Step-by-Step Guide in R

Understanding Contour Plots and the Challenges of Adding a Dot

Contour plots are a powerful tool for visualizing two-dimensional data, particularly in fields like geography, meteorology, and computer graphics. In this article, we’ll delve into contour plotting with R’s filled.contour function and explore how to add a dot to a filled contour plot.

Background: How Contour Plots Work

A contour plot displays values of a two-dimensional field as lines connecting points on the surface at constant levels. The color palette used in the plot can vary depending on the chosen method. R’s filled.contour function creates a filled contour plot, where each line is replaced by a filled area.

R’s `filled.contour` Function

The filled.contour function is part of R’s graphics package and is used to create filled contour plots. It takes several arguments:

x and y: The coordinates of the data points.
color.palette: A vector of colors used for the plot.
asp: A scaling factor that resizes the aspect ratio of the plot.

Adding a Dot to a Filled Contour Plot

Adding a dot to a filled contour plot without using ggplot2 requires using the plot.axes argument in combination with the axis function. This allows us to customize specific aspects of the plot.

Using `plot.axes`

The plot.axes argument is used to specify custom axes and plot elements for a given area of the plot. In this case, we’ll use it to add a dot at the location of the maximum point in the data.

Getting Coordinates of Maximum

To find the coordinates of the maximum point, we first need to identify which point corresponds to the maximum value in the data. We can do this using R’s built-in functions which and arr.ind.

# Get coordinates of maximum
max.point = (which(volcano == max(volcano), arr.ind = TRUE) - 1) / 
            (dim(volcano) - 1)

Using `plot.axes` to Add a Dot

Now that we have the coordinates of the maximum point, we can use the plot.axes argument in combination with the points function to add a dot at this location.

# Use plot.axes argument to plot maximum point
filled.contour(volcano, color.palette = terrain.colors, asp = 0.5,
               plot.axes={
                 points(max.point, col = "red", pch = 16)
                 axis(side = 1)
                 axis(side = 2)
                 }
               )

In the code above, we add a dot at the max.point location with a red color and 16-dot shape.

Example: Adding a Dot to a Contour Plot

Below is an example of how you might use these steps to create a contour plot with a dot:

# Load necessary libraries
library(RColorBrewer)

# Create volcano data
volcano = matrix(rnorm(10000), nrow = 100, ncol = 10)

# Get coordinates of maximum
max.point = (which(volcano == max(volcano), arr.ind = TRUE) - 1) / 
            (dim(volcano)[1] - 1)

# Use plot.axes argument to plot maximum point
filled.contour(volcano, color.palette = terrain.colors, asp = 0.5,
               plot.axes={
                 points(max.point, col = "red", pch = 16)
                 axis(side = 1)
                 axis(side = 2)
                 }
               )

Comparison to ggplot2

Here is an example of how you can achieve the same result using ggplot2:

# Load necessary libraries
library(tidyverse)

# Create volcano data
volcano = matrix(rnorm(10000), nrow = 100, ncol = 10)

# Convert volcano to dataframe
df = as.data.frame(t(volcano)) %>% 
    rownames_to_column(var = "row") %&gt;% 
    gather(col, value, -row) %&gt;% 
    mutate(col = (as.numeric(gsub("V", "", col)) - 1) / 
            (nrow(volcano) - 1),
           row = (as.numeric(row) - 1) / 
              (ncol(volcano) - 1))

# Create contour plot with dot
df %&gt;% 
  ggplot(aes(col, row, z = value)) +
    geom_raster(aes(fill = value)) +
    geom_contour(colour = "grey50", size = 0.2) +
    geom_point(data = df %&gt;% filter(value == max(value)), 
               colour = "red", shape = 16, size = 2) +
    coord_fixed(ratio = ncol(volcano)/nrow(volcano), expand = FALSE) +
    scale_fill_gradient2(low = terrain.colors(3)[1], mid = terrain.colors(3)[2],
                         high = terrain.colors(3)[3], midpoint = mean(volcano)) +
    theme_minimal()

Conclusion

Adding a dot to a filled contour plot in R requires using the plot.axes argument with custom axes and plot elements. This approach provides more flexibility than simply adding a point after the plot is created.

By understanding how contour plots work and using the plot.axes argument effectively, you can customize your plots to better communicate insights from your data.

Advice for Future Use

If you need to create multiple plots with different locations of interest, consider using an approach that doesn’t rely on manual adjustments or by iterating through each plot individually.

Last modified on 2024-09-08