Scatter Plots - R Base Graphs
Previously, we described the essentials of R programming and provided quick start guides for importing data into R.
Launch RStudio as described here: Running RStudio and setting up your working directory
Prepare your data as described here: Best practices for preparing your data and save it in an external .txt tab or .csv files
Import your data into R as described here: Fast reading of data from txt|csv files into R: readr package.
Here, we’ll use the R built-in mtcars data set.
R base scatter plot: plot()
x <- mtcars$wt y <- mtcars$mpg # Plot with main and axis titles # Change point shape (pch = 19) and remove frame. plot(x, y, main = "Main title", xlab = "X axis title", ylab = "Y axis title", pch = 19, frame = FALSE) # Add regression line plot(x, y, main = "Main title", xlab = "X axis title", ylab = "Y axis title", pch = 19, frame = FALSE) abline(lm(y ~ x, data = mtcars), col = "blue")
# Add loess fit plot(x, y, main = "Main title", xlab = "X axis title", ylab = "Y axis title", pch = 19, frame = FALSE) lines(lowess(x, y), col = "blue")
Enhanced scatter plots: car::scatterplot()
The function scatterplot() [in car package] makes enhanced scatter plots, with box plots in the margins, a non-parametric regression smooth, smoothed conditional spread, outlier identification, and a regression line, …
- Install car package:
- Use scatterplot() function:
library("car") scatterplot(wt ~ mpg, data = mtcars)
The plot contains:
- the points
- the regression line (in green)
- the smoothed conditional spread (in red dashed line)
- the non-parametric regression smooth (solid line, red)
# Suppress the smoother and frame scatterplot(wt ~ mpg, data = mtcars, smoother = FALSE, grid = FALSE, frame = FALSE)
# Scatter plot by groups ("cyl") scatterplot(wt ~ mpg | cyl, data = mtcars, smoother = FALSE, grid = FALSE, frame = FALSE)
It’s also possible to add labels using the following arguments:
- labels: a vector of point labels
- id.n, id.cex, id.col: Arguments for labeling points specifying the number, the size and the color of points to be labelled.
# Add labels scatterplot(wt ~ mpg, data = mtcars, smoother = FALSE, grid = FALSE, frame = FALSE, labels = rownames(mtcars), id.n = nrow(mtcars), id.cex = 0.7, id.col = "steelblue", ellipse = TRUE)
## Mazda RX4 Mazda RX4 Wag Datsun 710 Hornet 4 Drive Hornet Sportabout Valiant ## 1 2 3 4 5 6 ## Duster 360 Merc 240D Merc 230 Merc 280 Merc 280C Merc 450SE ## 7 8 9 10 11 12 ## Merc 450SL Merc 450SLC Cadillac Fleetwood Lincoln Continental Chrysler Imperial Fiat 128 ## 13 14 15 16 17 18 ## Honda Civic Toyota Corolla Toyota Corona Dodge Challenger AMC Javelin Camaro Z28 ## 19 20 21 22 23 24 ## Pontiac Firebird Fiat X1-9 Porsche 914-2 Lotus Europa Ford Pantera L Ferrari Dino ## 25 26 27 28 29 30 ## Maserati Bora Volvo 142E ## 31 32
Other arguments can be used such as:
- log to produce log axes. Allowed values are log = “x”, log = “y” or log = “xy”
- boxplots: Allowed values are:
- “x”: a box plot for x is drawn below the plot
- “y”: a box plot for y is drawn to the left of the plot
- “xy”: both box plots are drawn
- “” or FALSE to suppress both box plots.
- ellipse: if TRUE data-concentration ellipses are plotted.
3D scatter plots
To plot a 3D scatterplot the function scatterplot3D [in scatterplot3D package can be used].
The following R code plots a 3D scatter plot using iris data set.
## Sepal.Length Sepal.Width Petal.Length Petal.Width Species ## 1 5.1 3.5 1.4 0.2 setosa ## 2 4.9 3.0 1.4 0.2 setosa ## 3 4.7 3.2 1.3 0.2 setosa ## 4 4.6 3.1 1.5 0.2 setosa ## 5 5.0 3.6 1.4 0.2 setosa ## 6 5.4 3.9 1.7 0.4 setosa
# Prepare the data set x <- iris$Sepal.Length y <- iris$Sepal.Width z <- iris$Petal.Length grps <- as.factor(iris$Species) # Plot library(scatterplot3d) scatterplot3d(x, y, z, pch = 16)
# Change color by groups # add grids and remove the box around the plot # Change axis labels: xlab, ylab and zlab colors <- c("#999999", "#E69F00", "#56B4E9") scatterplot3d(x, y, z, pch = 16, color = colors[grps], grid = TRUE, box = FALSE, xlab = "Sepal length", ylab = "Sepal width", zlab = "Petal length")
- Read more about static and interactive 3D scatter plot:
Create a scatter plot:
- Using R base function:
with(mtcars, plot(wt, mpg, frame = FALSE))
- Using car package:
car::scatterplot(wt ~ mpg, data = mtcars, smoother = FALSE, grid = FALSE)
- 3D scatter plot:
library(scatterplot3d) with(iris, scatterplot3d(x = Sepal.Length, y = Sepal.Width, z = Petal.Length, pch = 16, grid = TRUE, box = FALSE) )
This analysis has been performed using R statistical software (ver. 3.2.4).
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