Recreating the vaccine heatmap in plotly 4.0 with R

Recreating popular viz
Polio Vaccine

Robert Mitchell


October 14, 2015

This took me a while to figure out how to implement. Since plotly 4.0+ is so different1 and the documentation is still rolling out2 I wanted to challenge myself to make something complicated to better understand how things have changed. I think the Impact of Vaccines visualizations are some of the best examples of how powerful data visualization can be–it becomes difficult to mount an counter argument after seeing them. So, here goes!

In order to get the data for this visualization you will need to create a free account over at Project Tyco. You can download all the datasets if you’d like but I’m just going to use the Polio data set. These are the packages that I’m using:

Load Packages


I should probably get in the habit of inspecting the csv files in vim before loading them so I can decide how I want to read in the file. In this case, using the readr package, you’ll need to set a couple of options: first you’ll need to set the skip argument to 2 since there are two lines of metadata about the data set. The second argument is na, which takes a simple vector for weirdly encoded NA values. In this data set, - is used for NA, so you’ll set the na argument to c("-", "NA") to ensure those values are handled correctly. The third arugment to set is col_types, which is an awesome way to control your data types during reading so you do less old-fashioned type conversion à la df$x <- as.numeric(df$x), which I don’t think anyone likes doing. readr’s heuristic guesses correctly for all columns except the variables for ALASKA and HAWAII. I’m not exactly sure why, but my guess is that the 0.00 values mess with the NA checks that readr performs. Luckily, we don’t have to know the why since we can just change those two and leave readr to do its job on the others:

Read in the data

polio <- read_csv("POLIO_Incidence_1928-1969_20160904215505.csv", 
                  skip = 2, na = c("-", "NA"),
                  col_types = list(
                    ALASKA = col_double(),
                    HAWAII = col_double()

Now, the way this data set is structures is super weird. In order to get it into a tidy format we’ll need to use tidyr; specifically the gather function. But I don’t want to pass through all the variable names, so with a little lazy figuring out, I just kept changing the numbers until I found the right range in numbers with dplyr’s select function since it uses the same start_row:end_row notation:

Find the index for the columns you want to gather with tidyr

polio %>% select(3:53) %>% head()

Use gather to transform data, rename columns, and make sure cases is numeric

polio <- polio %>% gather(3:53, key="state", value="cases") 
polio <- rename(polio, year = YEAR, week = WEEK, state = state, cases = cases)

This is a quick function to get the states data in the right format to use R’s built in data, which I found online. I’ve never used the match function before, but this seemed to work really well except for DC, which I’m using dplyr’s if_else function to correct. This is a sloppy function but it works for this data.

Fix all caps

fix_state_names <- function(data) {
  lower <- str_to_lower(data)
  title <- str_to_title(lower)
  alter <-[match(title,]
  out <- if_else(, "DC", alter)

Apply the fix_state_names function to the state column

polio$state <- map_chr(polio$state, fix_state_names)

We need to sum all the cases in a given year by state, but if the whole year contains NA values, I’m going to give it a value of 0.

group_by to sum all the cases for a year and then ungroup data frame

polio <- polio %>% 
  group_by(year, state) %>%
  summarise(totals = if_else(all(, 0, sum(cases, na.rm = T))) %>%
`summarise()` has grouped output by 'year'. You can override using the `.groups`

Set margins for plot

m <- list(
  l = 40,
  r = 50,
  b = 50,
  t = 50,
  pad = 4

You can create a custom colorscale in a lot of different ways, but I found creating a data frame with tribble to be the easiest way. Trying to replicate this colorscale was difficult because the blues, greens, and yellow colors are only representing values between 0-10% of the total values, so I had to keep changing things until it looked right. Using tribble helps because it is easier to line things up rather than counting vector locations with your finger on the screen (does anyone else do that!?).

Create custom colorscale

polio_color <- tribble(
  ~range, ~hex,
  0.000,  "#e7f0fa",
  0.025,  "#c9e2f6",
  0.045,  "#95cbee",
  0.065,  "#0099dc",
  0.085,  "#4ab04a",
  0.105,  "#ffd73e",
  0.150,  "#eec73a",
  0.300,  "#e29421",
  0.450,  "#f05336",
  1.000,  "#ce472e"

Plot the data

polio %>%
    x = ~year, y = ~state,
    height = 1000, width = 950) %>%
    z = ~totals, zmin = 0, zmax = 190,
    text = ~paste(
      "Year: ", year, "<br>State: ", state,
      "<br>Total Cases: ", totals),
    hoverinfo = "text", colorscale = polio_color, showscale = F,
    opacity = 0.85) %>%
    "Vaccine Introduced", x = 1957.5, y = -1.5, showarrow = F) %>%
    x = 1955, xend = 1955, y = ~state[3], yend = ~state[49],
    line = list(width = 2, color = "black"),
    name = "1955", hoverinfo = "text",
    text = paste("Vaccine Introduced: 1955")) %>%
    title = "Polio",
    xaxis = list(title = "", nticks = 10),
    yaxis = list(title = "", autorange = "reversed"),
    margin = m, autosize = F)

There’s a lot going on here, but the code is not too verbose (at least I don’t think). I add the year and state data to the regular plot_ly function while placing the z data that transforms it into a heatmap in add_heatmap. Even though I’m pushing the annotation outside of the plot, plotly doesn’t add any more y ticks. However, in add_segments if I used y = ~min(state), yend = ~max(state) there would have been two extra y ticks on the bottom (0 and 1). This is annoying and I tried many different things to get everything to behave nicely but it’s hard to get a heatmap and lines and annotations to work well together. My workaround is to just make the segment line a little shorter, but I don’t think it looks too bad.

Let me know if you have any thoughts about improving things in the comments!



  2. git clone and git pull often:↩︎