Exercise 4 - Solutions

Functions

  1. Create a file that will contain your functions.

  2. In the file, write a function that takes a dataframe and a numerical value and returns a boxplot. Do not worry about error or warning handling yet. NB If you modify the function script, be sure to save it and source it again so that your updates are reflected in the main script.

aes_string allows the function to dynamically reference a column name from the dataframe.

Example: aes_string("colname")

Main script

  1. Create a Quarto document and start by loading relevant packages.
library(tidyverse)
Warning: pakke 'ggplot2' blev bygget under R version 4.2.3
Warning: pakke 'tibble' blev bygget under R version 4.2.3
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library(glue)
  1. Source the function script into the Quarto document.
source('solution4_functions.R')
  1. Load data from the .rds you created in Exercise 2.
diabetes_glucose <- read_rds('../out/diabetes_glucose.rds')
  1. Run the boxplot function for the diabetes dataset and the Age variable.
boxplot(df = diabetes_glucose, var_num = 'Age')
Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more information.
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  1. In a for-loop, run the boxplot function for the diabetes dataset and each of the numerical variables in the script.
numerical_columns <- sapply(diabetes_glucose, is.numeric)
numerical_colnames <- names(diabetes_glucose)[numerical_columns]
for (var_num in numerical_colnames){
  
  p <- boxplot(df = diabetes_glucose, var_num = var_num)
  print(p)
  # ggsave(paste0("../out/boxplot_", var_num,".png"))
  
}
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  1. Go back to your function script. Create a function that takes a dataframe and a categorical value and returns a bar plot.

  2. Run the function on the Sex variable.

bar_plot(df = diabetes_glucose, var_cat = 'Sex')
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  1. In a for-loop, run the bar plot function for the diabetes dataset and each of the categorical variables in the script.
categorical_columns <- sapply(diabetes_glucose, is.character)
categorical_colnames <- names(diabetes_glucose)[categorical_columns]
for (var_cat in categorical_colnames){
  
  p <- bar_plot(df = diabetes_glucose, var_cat = var_cat)
  print(p)
  # ggsave(paste0("../out/bar_plot_", var_cat,".png"))
  
}
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  1. It’s time for a fun exercise! Customize your plot functions by adding a theme, colors and labels. Add a ggsave statement in your for-loops to recreate and save your plots.

Functions and error handling

  1. In your function script, copy the function you created in Exercise 2 and modify it so that it generates an error if var_num is assigned a non-numerical argument.

When checking the class of the variables, make sure that they are in vector format. Have a look at Presentation 1 if you are unsure of how to access a variable in a data frame as a vector.

is.numeric(vector)
  1. Test the function by using Sex as the numerical variable argument.
boxplot_2(df = diabetes_glucose, var_num = 'Sex')
# Gives an error.

  1. Use the same logic for the function you created in Exercise 8.

  2. Test the function by using Age as the categorical variable argument.

bar_plot_2(df = diabetes_glucose, var_cat = 'Age')
# Gives an error.
  1. In Exercise 7, a boxplot have made for the ID variable if you simply looped over all the numcerical values. Avoid this using an if-statement.
for (var_num in numerical_colnames){
  
  if (var_num != 'ID'){
    
    p <- boxplot(df = diabetes_glucose, var_num = var_num)
    print(p)
    
  }
  
}
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  1. Make a function that takes an ID and outputs a graph of the glucose measurement over time. There are several way to do this depending on how generalized your function is. The more generalized, the more difficult.

Remember that you need to put backticks when you access a colname with spaces.

When using aes_string, you need backticks and quotation marks: aes_string("`colname with spaces`").

  1. Run the function on your favorite ID.
df <- diabetes_glucose %>% unnest(OGTT)

glucose_measurement_id_plot(df = df, id = "12109")
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  1. Inspired by Exercise 3.13, create a function that takes a dataframe and a categorical variable as input, calculates the mean glucose levels over time for each category, and produces a line plot showing the mean glucose measurements across time points.

The function requires the column name to be passed as a string. However, not all tidyverse functions can directly handle column names in this format. Fortunately, there is a workaround. For example, the group_by() function can dynamically reference a column name provided as a string using .data[[...]]:

var_cat <- "Age"

df %>% 
    group_by(Measurement, .data[[var_cat]])

Here, .data refers to the data frame being used — in this case, df.

Also, you might get a warning like this You can override using the .groups argument. This can be solved adding .groups = "drop" to the summerize function.

  1. Run the function with Sex as input.
glucose_measurement_mean_plot(df = df, var_cat = 'Sex')
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  1. In a for-loop, run the function on all categorical variables in the data frame. Between which groups do you visually notice the largest differences in the mean OGTT?
for (var_cat in categorical_colnames){
  
  p <- glucose_measurement_mean_plot(df = df, var_cat = var_cat)
  print(p)
  
}
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Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database

Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database

Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database

Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database

Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database

Last. Render you document and review the generated html. If you get errors, correct them and re-render.