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Simple tricks for Debugging Pipes (within magrittr, base R or ggplot2)

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You know it, I’m sure: You are developing a data transformation using lots of pipes. Then you need to remove one or more lines. You do this using comments.

So far so good. But if it’s the last line you want to remove a simple comment will produce an error because of the trailing pipe symbol at the end of the second to last line.

Here’s a solution:

Pipes

Magrittr

Let’s say you are computing something like this:

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options(tidyverse.quiet = TRUE)
library(tidyverse)
options(dplyr.summarise.inform = FALSE)

starwars %>% 
  mutate(
   mean_height = mean(height, na.rm = TRUE)
  ) %>% 
  group_by(species, gender) %>% 
  summarize(
    mean_height_species_gender = mean(height, na.rm = TRUE),
    mean_height = first(mean_height)
  ) %>% 
  mutate(
    diff_mean_height = mean_height_species_gender - mean_height
  ) %>% 
  select(gender, species, diff_mean_height) %>% 
  pivot_wider(names_from = 'gender', values_from = 'diff_mean_height', values_fill = NA) 

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## # A tibble: 38 x 4
## # Groups:   species [38]
##    species   masculine feminine  `NA`
##    <chr>         <dbl>    <dbl> <dbl>
##  1 Aleena       -95.4     NA       NA
##  2 Besalisk      23.6     NA       NA
##  3 Cerean        23.6     NA       NA
##  4 Chagrian      21.6     NA       NA
##  5 Clawdite      NA       -6.36    NA
##  6 Droid        -34.4    -78.4     NA
##  7 Dug          -62.4     NA       NA
##  8 Ewok         -86.4     NA       NA
##  9 Geonosian      8.64    NA       NA
## 10 Gungan        34.3     NA       NA
## # … with 28 more rows

Now you want to skip the last step pivoting the result. If you just comment out the last line, you’ll get an error:

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starwars %>% 
  mutate(
   mean_height = mean(height, na.rm = TRUE)
  ) %>% 
  group_by(species, gender) %>% 
  summarize(
    mean_height_species_gender = mean(height, na.rm = TRUE),
    mean_height = first(mean_height)
  ) %>% 
  mutate(
    diff_mean_height = mean_height_species_gender - mean_height
  ) %>% 
  select(gender, species, diff_mean_height) %>% 
  # pivot_wider(names_from = 'gender', values_from = 'diff_mean_height', values_fill = NA) 

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## Error: <text>:15:0: unexpected end of input
## 13:   select(gender, species, diff_mean_height) %>% 
## 14:   # pivot_wider(names_from = 'gender', values_from = 'diff_mean_height', values_fill = NA) 
##    ^

But if you use identity() as your last step everything is fine:

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starwars %>% 
  mutate(
   mean_height = mean(height, na.rm = TRUE)
  ) %>% 
  group_by(species, gender) %>% 
  summarize(
    mean_height_species_gender = mean(height, na.rm = TRUE),
    mean_height = first(mean_height)
  ) %>% 
  mutate(
    diff_mean_height = mean_height_species_gender - mean_height
  ) %>% 
  select(gender, species, diff_mean_height) %>% 
  # pivot_wider(names_from = 'gender', values_from = 'diff_mean_height', values_fill = NA) %>% 
  identity()

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## # A tibble: 42 x 3
## # Groups:   species [38]
##    gender    species   diff_mean_height
##    <chr>     <chr>                <dbl>
##  1 masculine Aleena              -95.4 
##  2 masculine Besalisk             23.6 
##  3 masculine Cerean               23.6 
##  4 masculine Chagrian             21.6 
##  5 feminine  Clawdite             -6.36
##  6 feminine  Droid               -78.4 
##  7 masculine Droid               -34.4 
##  8 masculine Dug                 -62.4 
##  9 masculine Ewok                -86.4 
## 10 masculine Geonosian             8.64
## # … with 32 more rows

Base R (R >= 4.1.0)

This trick will also work with the new base R pipes:

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starwars |> 
  mutate(
   mean_height = mean(height, na.rm = TRUE)
  ) |> 
  group_by(species, gender) |> 
  summarize(
    mean_height_species_gender = mean(height, na.rm = TRUE),
    mean_height = first(mean_height)
  ) |>
  mutate(
    diff_mean_height = mean_height_species_gender - mean_height
  ) |>
  select(gender, species, diff_mean_height) |>
  # pivot_wider(names_from = 'gender', values_from = 'diff_mean_height', values_fill = NA) |>
  identity()

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## # A tibble: 42 x 3
## # Groups:   species [38]
##    gender    species   diff_mean_height
##    <chr>     <chr>                <dbl>
##  1 masculine Aleena              -95.4 
##  2 masculine Besalisk             23.6 
##  3 masculine Cerean               23.6 
##  4 masculine Chagrian             21.6 
##  5 feminine  Clawdite             -6.36
##  6 feminine  Droid               -78.4 
##  7 masculine Droid               -34.4 
##  8 masculine Dug                 -62.4 
##  9 masculine Ewok                -86.4 
## 10 masculine Geonosian             8.64
## # … with 32 more rows

ggplot2

The same problem may occur building ggplots:

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iris %>% 
  ggplot(aes(Sepal.Length, Sepal.Width, color = Species, group = Species)) +
  geom_point() +
  geom_smooth(method = "lm", se = FALSE, formula = "y ~ x") +
  # facet_wrap(~Species) +
  NULL

As you can see, I’ve added NULl at the end of the ggplot2-pipe. So I comment out the line before without trouble.

RStudio Plugin breakerofchains

There’s also a plugin for RStudio called breakerofchains. Using this plugin you can set your cursor onto any line of sequence of pipes. When you call the plugin the code is run up to the line your cursor is.

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