plot lm() results with ggplot2 in R from Susan E Johnston Blog

Susan E Johnston

Postdoc in Ecological Genetics, University of Turku, Finland

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A quick and easy function to plot lm() results with ggplot2 in R

August 9, 2012 2 Comments

Sometimes it's nice to quickly visualise the data that went into a simple linear regression, especially when you are performing lots of tests at once. Here is a quick and dirty solution with ggplot2 to create the following plot:

Let's try it out using the iris dataset in R:

data(iris)
head(iris)

##   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

Create fit1, a linear regression of Sepal.Length and Petal.Width. Normally we would quickly plot the data in R base graphics:

fit1 <- lm(Sepal.Length ~ Petal.Width, data = iris)
summary(fit1)

## 
## Call:
## lm(formula = Sepal.Length ~ Petal.Width, data = iris)
## 
## Residuals:
##    Min       1Q      Median     3Q       Max 
## -1.3882   -0.2936   -0.0439   0.2643   1.3452 
## 
## Coefficients:
##               Estimate Std. Error t value Pr(>|t|) 
## (Intercept)    4.7776    0.0729    65.5   <2e-16 ***
## Petal.Width    0.8886    0.0514    17.3   <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 
## 
## Residual standard error: 0.478 on 148 degrees of freedom
## Multiple R-squared: 0.669, Adjusted R-squared: 0.667 
## F-statistic: 299 on 1 and 148 DF, p-value: <2e-16 
## 

plot(Sepal.Length ~ Petal.Width, data = iris)
abline(fit1)

However, we can create a quick function that will pull the data out of a linear regression, and return important values (R-squares, slope, intercept and P value) at the top of a nice ggplot graph with the regression line:

ggplotRegression <- function (fit) {

require(ggplot2)

ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1])) + 
  geom_point() +
  stat_smooth(method = "lm", col = "red") +
  opts(title = paste("Adj R2 = ",signif(summary(fit)$adj.r.squared, 5),
                     "; Intercept =",signif(fit$coef[[1]],5 ),
                     "; Slope =",signif(fit$coef[[2]], 5),
                     "; P =",signif(summary(fit)$coef[2,4], 5)))
}

After specifying this function, all you would have to run is:

fit1 <- lm(Sepal.Length ~ Petal.Width, data = iris)
ggplotRegression(fit1)

or even just

ggplotRegression(lm(Sepal.Length ~ Petal.Width, data = iris))

Disclaimer: This is not suitable for non-normal distributions or categorical variables!

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About susanejohnston
Postdoctoral researcher at the University of Turku, interested in ecology, evolution and genetics.