A note to science journal editors: require better visuals

In reviewing a new small-scale study of the Moderna vaccine, I found this chart:

Modernahalfdoses_fig3a

This style of charts is quite common in scientific papers. And they are horrible. It irks me to think that some authors are forced to adopt such styles.

The study's main goal is to compare two half doses to two full doses of the Moderna vaccine. (To understand the science, read the post on my book blog.) The participants were stratified by age group. The vaccine is expected to work better for younger people than for older people. The point of the study isn't to measure the difference by age group, and so the age-group dimension is secondary.

Upon recognizing that, I reduce the number of colors from 4 to 2:

Junkcharts_redo_modernahalfdoses_1

Halving the number of colors presents no additional difficulty. The reader spends less time cross-referencing.

The existence of the Pbo (placebo) and Conv (convalescent plasma) columns on the sides is both unsightly and suboptimal. The "Conv" serves as a reference level for the amount of antibodies the vaccine stimulates in people. A better way to display reference levels is using reference lines.

Junkcharts_redo_modernahalfdoses_2color

The biggest problem with the chart is the log scale on the vertical axis. This isn't even a log-10 but a log-2. (Each tick is a doubling of value.)

Take the first set of columns as an example. The second column is clearly less than twice the height of the first column, and yet 25 is 3.5 times bigger than 7.  The third column is also visually less than double the size of the second column, and yet 189 is 7.5 times bigger than 25. The areas (heights) of the columns do not convey the right information about relative sizes of the underlying data.

Here's an amusing observation. The brown area shaded below is half of the entire area of the chart - if we reverted it to a linear scale. And yet there is not a single data point above 250 in the data so the brown area is entirely empty.

Junkcharts_redo_modernahalfdoses_logscale

An effect of a log scale is to compress the larger values of a dataset. That's what you're seeing here.

I now revisualize using dotplots:

Junkcharts_redo_modernahalfdoses_dotplotlinear

The version on the left retains the log scale while the right one (pun intended) reverts to the linear scale.

The biggest effect by far is the spike of antibodies between day 29 and 43 - which is after the second shot is administered. (For Moderna, the second shot is targeted for day 28.) In fact, it is during that window that the level of antibodies went from below the "conv" level (i.e. from natural infection) to far above.

The log-scale version buries this finding because it squeezes the large numbers on the chart. In addition, it artificially pulls the small numbers toward the "Conv" level. On the right chart, the second dot for 18-54, full doses is only at half the level of "Conv"  but it looks tantalizing close to the "Conv" level on the left chart.

The authors of the study also claim that there is negligible dropoff by 30 days after the second dose, i.e. between the third and fourth dots in each set. That may be so on the log-scale chart but on the linear chart, we see a moderate reduction. I don't believe the size of this study allows us to make a stronger conclusion but the claim of no dropoff is dubious.

The left chart also obscures the age-group differences. It appears as if all four sets show roughly the same pattern. With the linear scale, we notice that the vaccine clearly works better for the younger subgroup. As I discussed on the book blog, no one actually knows what level of antibodies constitutes "protection," and so I can't say whether that age-group difference has practical significance.

***

I recommend using log scales sparingly and carefully. They are a source of much mischief and misadventure.

 

 

 


Same data + same chart form = same story. Maybe.

We love charts that tell stories.

Some people believe that if they situate the data in the right chart form, the stories reveal themselves.

Some people believe for a given dataset, there exists a best chart form that brings out the story.

An implication of these beliefs is that the story is immutable, given the dataset and the chart form.

If you use the Trifecta Checkup, you already know I don't subscribe to those ideas. That's why the Trifecta has three legs, the third is the question - which is related to the message or the story.

***

I came across the following chart by Statista, illustrating the growth in Covid-19 cases from the start of the pandemic to this month. The underlying data are collected by WHO and cover the entire globe. The data are grouped by regions.

Statista_avgnewcases

The story of this chart appears to be that the world moves in lock step, with each region behaving more or less the same.

If you visit the WHO site, they show a similar chart:

WHO_horizontal_casesbyregion

On this chart, the regions at the bottom of the graph (esp. Southeast Asia in purple) clearly do not follow the same time patterns as Americas (orange) or Europe (green).

What we're witnessing is: same data, same chart form, different stories.

This is a feature, not a bug, of the stacked area chart. The story is driven largely by the order in which the pieces are stacked. In the Statista chart, the largest pieces are placed at the bottom while for WHO, the order is exactly reversed.

(There are minor differences which do not affect my argument. The WHO chart omits the "Other" category which accounts for very little. Also, the Statista chart shows the smoothed data using 7-day averaging.)

In this example, the order chosen by WHO preserves the story while the order chosen by Statista wipes it out.

***

What might be the underlying question of someone who makes this graph? Perhaps it is to identify the relative prevalence of Covid-19 in different regions at different stages of the pandemic.

Emphasis on the word "relative". Instead of plotting absolute number of cases, I consider plotting relative number of cases, that is to say, the proportion of cases in each region at given times.

This leads to a stacked area percentage chart.

Junkcharts_redo_statistawho_covidregional

In this side-by-side view, you see that this form is not affected by flipping the order of the regions. Both charts say the same thing: that there were two waves in Europe and the Americas that dwarfed all other regions.

 

 


Making graphics last over time

Yesterday, I analyzed the data visualization by the White House showing the progress of U.S. Covid-19 vaccinations. Here is the chart.

Whgov_proportiongettingvaccinated

John who tweeted this at me, saying "please get a better data viz".

I'm happy to work with them or the CDC on better dataviz. Here's an example of what I do.

Junkcharts_redo_whgov_usvaccineprogress

Obviously, I'm using made-up data here and this is a sketch. I want to design a chart that can be updated continuously, as data accumulate. That's one of the shortcomings of that bubble format they used.

In earlier months, the chart can be clipped to just the lower left corner.

Junkcharts_redo_whgov_usvaccineprogress_2


Circular areas offer misleading cues of their underlying data

John M. pointed me on Twitter to this chart about the progress of U.S.'s vaccination campaign:

Whgov_proportiongettingvaccinated

This looks like a White House production, retweeted by WHO. John is unhappy about this nested bubble format, which I'll come back to later.

Let's zoom in on what matters:

Whgov_proportiongettingvaccinated_clip

An even bigger problem with this chart is the Q corner in our Trifecta Checkup. What is the question they are trying to address? It would appear to be the proportion of population that has "already received [one or more doses of] vaccine". And the big words tell us the answer is 8 percent.

_junkcharts_trifectacheckupBut is that really the question? Check out the dark blue circle. It is labeled "population that has already received vaccine" and thus we infer this bubble represents 8 percent. Now look at the outer bubble. Its annotation is "new population that received vaccine since January 27, 2021". The only interpretation that makes sense is that 8 percent  is not the most current number. If that is the case, why would the headline highlight an older statistic, and not the most up-to-date one?

Perhaps the real question is how fast is the progress in vaccination. Perhaps it took weeks to get to the dark circle and then days to get beyond. In order to improve this data visualization, we must first decide what the question really is.

***

Now let's get to those nested bubbles. The bubble chart is a format that is not "sufficient," by which I mean the visual by itself does not convey the data without the help of aids such as labels. Try to answer the following questions:

Junkcharts_whgov_vaccineprogress_bubblequiz

In my view, if your answer to the last question is anything more than 5 seconds, the dataviz has failed. A successful data visualization should not make readers solve puzzles.

The first two questions depict the confusing nature of concentric circle diagrams. The first data point is coded to the inner circle. Where is the second data point? Is it encoded to the outer circle, or just the outer ring?

In either case, human brains are not trained to compare circular areas. For question 1, the outer circle is 70% larger than the smaller circle. For question 2, the ring is 70% of the area of the dark blue circle. If you're thinking those numbers seem unreasonable, I can tell you that was my first reaction too! So I made the following to convince myself that the calculation was correct:

Junkcharts_whgov_vaccineprogress_bubblequiz_2

Circular areas offer misleading visual cues, and should be used sparingly.

[P.S. 2/10/2021. In the next post, I sketch out an alternative dataviz for this dataset.]