TrelliscopeJS

Ryan Hafen

Hafen Consulting, LLC

Small Multiples

A series of similar plots, usually each based on a different slice of data, arranged in a grid

"For a wide range of problems in data presentation, small multiples are the best design solution."

Edward Tufte (Envisioning Information)

This idea was formalized and popularized in S/S-PLUS and subsequently R with the trellis and lattice packages

Advantages of Small Multiple Displays

• Avoid overplotting
• Work with big or high dimensional data
• It is often critical to the discovery of a new insight to be able to see multiple things at once
  • Our brains are good at perceiving simple visual features like color or shape or size and they do it amazingly fast without any conscious effort
  • We can tell immediately when a part of an image is different from the rest, without really having to focus on it

Trelliscope:

Interactive Small Multiple Display

• Small multiple displays are useful when visualizing data in detail
• But the number of panels in a display can be potentially very large, too large to view all at once

Motivating Example

Gapminder

Suppose we want to understand mortality over time for each country

Observations: 1,704
Variables: 6
$ country   <fctr> Afghanistan, Afghanistan, Afghanistan, Afghanistan, Afgh...
$ continent <fctr> Asia, Asia, Asia, Asia, Asia, Asia, Asia, Asia, Asia, As...
$ year      <int> 1952, 1957, 1962, 1967, 1972, 1977, 1982, 1987, 1992, 199...
$ lifeExp   <dbl> 28.801, 30.332, 31.997, 34.020, 36.088, 38.438, 39.854, 4...
$ pop       <int> 8425333, 9240934, 10267083, 11537966, 13079460, 14880372,...
$ gdpPercap <dbl> 779.4453, 820.8530, 853.1007, 836.1971, 739.9811, 786.113...

glimpse(gapminder)

https://www.gapminder.org/

qplot(year, lifeExp, data = gapminder, 
  color = country, geom = "line")

Yikes! There are a lot of countries...

qplot(year, lifeExp, data = gapminder, color = continent,
  group = country, geom = "line")

Still too much going on...

qplot(year, lifeExp, data = gapminder, color = continent,
  group = country, geom = "line") +
    facet_wrap(~ continent, nrow = 1)

That helped a little...

p <- qplot(year, lifeExp, data = gapminder, color = continent,
  group = country, geom = "line") +
    facet_wrap(~ continent, nrow = 1)
plotly::ggplotly(p)

This helps but there is still a lot of overplotting...

qplot(year, lifeExp, data = gapminder) + theme_bw() +
  facet_wrap(~ country + continent)

qplot(year, lifeExp, data = gapminder) + theme_bw() +
  facet_trelliscope(~ country + continent, nrow = 2, ncol = 7, width = 300)

open in new window

Note: this and future plots in this presentation are interactive - feel free to explore!

qplot(year, lifeExp, data = gapminder) + theme_bw() +
  facet_trelliscope(~ country + continent,
    nrow = 2, ncol = 7, width = 300, as_plotly = TRUE)

open in new window

TrelliscopeJS

JavaScript Library

R Package

trelliscopejs-lib

trelliscopejs

• Built using React
• Pure JavaScript
• Interface agnostic
• No special server requirements 

• htmlwidget interface to trelliscopejs-lib
• Evolved from older CRAN "trelliscope" package

devtools::install_github("hafen/trelliscopejs")

Creating Displays: 3 Interfaces

1. ggplot2

2. tidyverse

3. images

ggplot2 Interface

Turning a ggplot2 faceted display into a Trelliscope display is as easy as changing:

to:

facet_wrap()

or:

facet_grid()

facet_trelliscope()

facet_trelliscope() main arguments

• ~: conditioning variables
• name: the name of the display
• desc: a free text description of the display
• path: path in which the display files should be stored (multiple displays can be stored in the same path)
• height, width: original dimensions (in pixels) of each panel (actual size will vary based on user interactions)
• nrow, ncol: default layout of the panels (can be changed by the user)

ggplot2 cognostics

• All conditioning variables are naturally cognostics
• Any column that is fixed within each group will be added as a cognostic
• For numeric columns that vary within each group, cognostic summary statistics of those variables will be added
• Optionally setting auto_cog = TRUE will also compute cognostics based on the context of what is being plotted

ggplot2 auto_cogs

• Automatically compute cognostics based on the context of what is being plotted
• Work done by Barret Schloerke as part of his Ph.D. thesis (defense.schloerke.com)
• Implemented for ggplot2

Tidyverse Interface

• Create a data frame with one row per group, typically using Tidyverse group_by() and nest() operations
• Add a column of plots
  • TrelliscopeJS provides purrr map functions map_plot(), map2_plot(), pmap_plot() that you can use to create these
  • You can now use any graphics system to create the plot objects (ggplot2, htmlwidgets, etc.)
• Optionally add more columns to the data frame that will be used as cognostics - metrics with which you can interact with the panels
  • All atomic columns will be automatically used as cognostics
  • Map functions map_cog(), map2_cog(), pmap_cog() can be used for convenience to create columns of cognostics
• Simply pass the data frame in to trelliscope()

country_model <- function(df)
  lm(lifeExp ~ year, data = df)

by_country <- gapminder %>%
  group_by(country, continent) %>%
  nest() %>%
  mutate(
    model = map(data, country_model),
    resid_mad = map_dbl(model, function(x)
      mad(resid(x))))

by_country

Example adapted from "R for Data Science"

# A tibble: 142 × 5
       country continent              data    model resid_mad
        <fctr>    <fctr>            <list>   <list>     <dbl>
1  Afghanistan      Asia <tibble [12 × 4]> <S3: lm> 1.4058780
2      Albania    Europe <tibble [12 × 4]> <S3: lm> 2.2193278
3      Algeria    Africa <tibble [12 × 4]> <S3: lm> 0.7925897
4       Angola    Africa <tibble [12 × 4]> <S3: lm> 1.4903085
5    Argentina  Americas <tibble [12 × 4]> <S3: lm> 0.2376178
6    Australia   Oceania <tibble [12 × 4]> <S3: lm> 0.7934372
7      Austria    Europe <tibble [12 × 4]> <S3: lm> 0.3928605
8      Bahrain      Asia <tibble [12 × 4]> <S3: lm> 1.8201766
9   Bangladesh      Asia <tibble [12 × 4]> <S3: lm> 1.1947475
10     Belgium    Europe <tibble [12 × 4]> <S3: lm> 0.2353342
# ... with 132 more rows

Gapminder Example from "R for Data Science"

• One row per group
• Per-group data and models as "list-columns"

country_plot <- function(data, model) {
  figure(xlim = c(1948, 2011),
    ylim = c(10, 95), tools = NULL) %>%
    ly_points(year, lifeExp,
      data = data,
      hover = data) %>%
    ly_abline(model)
}

country_plot(by_country$data[[1]],
  by_country$model[[1]])

Plotting the Data and Model Fit for Each Group

We'll use the rbokeh package to make a plot function and apply it to the first row of our data

by_country <- by_country %>%
  mutate(plot = map2_plot(data, model, country_plot))

by_country

Example adapted from "R for Data Science"

# A tibble: 142 × 6
       country continent              data    model resid_mad         plot
        <fctr>    <fctr>            <list>   <list>     <dbl>       <list>
1  Afghanistan      Asia <tibble [12 × 4]> <S3: lm> 1.4058780 <S3: rbokeh>
2      Albania    Europe <tibble [12 × 4]> <S3: lm> 2.2193278 <S3: rbokeh>
3      Algeria    Africa <tibble [12 × 4]> <S3: lm> 0.7925897 <S3: rbokeh>
4       Angola    Africa <tibble [12 × 4]> <S3: lm> 1.4903085 <S3: rbokeh>
5    Argentina  Americas <tibble [12 × 4]> <S3: lm> 0.2376178 <S3: rbokeh>
6    Australia   Oceania <tibble [12 × 4]> <S3: lm> 0.7934372 <S3: rbokeh>
7      Austria    Europe <tibble [12 × 4]> <S3: lm> 0.3928605 <S3: rbokeh>
8      Bahrain      Asia <tibble [12 × 4]> <S3: lm> 1.8201766 <S3: rbokeh>
9   Bangladesh      Asia <tibble [12 × 4]> <S3: lm> 1.1947475 <S3: rbokeh>
10     Belgium    Europe <tibble [12 × 4]> <S3: lm> 0.2353342 <S3: rbokeh>
# ... with 132 more rows

Apply This Function to Every Row

A plot for each model

by_country %>%
  trelliscope(name = "by_country_lm", nrow = 2, ncol = 4)

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Images Interface

• Trelliscope can act as an interface to query a database of images
• You simply need a data frame with one column pointing to a URL or local image file
• If image is a URL: 
  • Wrap the column with img_panel()
  • This URL could also be a service that returns an image
• ​​If image is local:
  • Make sure the image files are located inside the display's directory and that the specified path is relative to that
  • Wrap the column with img_panel_local()

pokemon <- read_csv("http://bit.ly/plot_pokemon") %>%
  mutate_at(vars(matches("_id$")), as.character) %>%
  mutate(panel = img_panel(url_image))

pokemon

trelliscope(pokemon, name = "pokemon", nrow = 3, ncol = 6,
  state = list(labels = c("pokemon", "pokedex")))
​

data source

open in new window

read_csv("http://bit.ly/trs-mri") %>%
  mutate(img = img_panel(img)) %>%
  trelliscope("brain_MRI", nrow = 2, ncol = 5)

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Advanced Features

• Customizing cognostics using cog()
• Links as cognostics using cog_href()
• Linking across displays (new feature in dev branch)

Example: Home Prices

Monthly median price per square foot by state and county, 2001-2019

List Prices Over Time by County

county %>%
  filter(!is.na(price_sqft)) %>%
  group_by(county) %>%
  mutate(price_diff = max(price_sqft) - min(price_sqft)) %>%
  ungroup() %>%
  mutate(
    price_diff = cog(price_diff,
      desc = "difference between highest and lowest price"),
    wiki_link = cog_href(
      paste0("https://en.wikipedia.org/wiki/", county))
  ) %>%
  ggplot(aes(date, log10(price_sqft))) +
    geom_point() +
    theme_bw() +
    facet_trelliscope(~ county + state_code, nrow = 2, ncol = 5,
      name = "county_median_list_log10",
      desc = "monthly county median list price per square foot",
      group = "county",
      path = "~/Desktop/housing",
      width = 300, height = 500)

State-Level Display Linking to County-Level

state %>%
  filter(!is.na(price_sqft)) %>%
  mutate(
    counties_link = cog_disp_filter(
      "county_median_list",
      var = "state_code",
      val = state_code, default_label = TRUE)
  ) %>%
  ggplot(aes(date, price_sqft)) +
    geom_point() +
    theme_bw() +
    facet_trelliscope(~ state, nrow = 2, ncol = 5,
      name = "state_median_list",
      desc = "monthly state median list price per square foot",
      group = "state",
      path = "~/Desktop/housing",
      width = 300, height = 500)

For More Information

• Twitter: @hafenstats
• Blog: http://ryanhafen.com/blog
• Documentation: http://hafen.github.io/trelliscopejs
• Github: https://github.com/hafen/trelliscopejs

 

Most examples in this talk are reproducible after installing and loading the following packages: