Putting vaccine trials in boxes

Bloomberg Businessweek has a special edition about vaccines, and I found this chart on the print edition:

The chart's got a lot of white space. Its structure is a series of simple "treemaps," one for each type of vaccine. Though simple, such a chart burns a few brain cells.

Here, I've extracted the largest block, which corresponds to vaccines that work with the virus's RNA/DNA. I applied a self-sufficiency test, removing the data from the boxes. 

What proportion of these projects have moved from pre-clinical to Phase 1?  To answer this question, we have to understand the relative areas of boxes, since that's how the data are encoded. How many yellow boxes can fit into the gray box?

It's not intuitive. We'd need a ruler to do this task properly.

Then, we learn that the gray box is exactly 8 times the size of the yellow box (72 projects are pre-clinical while 9 are in Phase I). We can cram eight yellows into the gray box. Imagine doing that, and it's pretty clear the visual elements fail to convey the meaning of the data.

Self-sufficiency is the idea that a data graphic should not rely on printed data to convey its meaning; the visual elements of a data graphic should bear much of the burden. Otherwise, use a data table. To test for self-sufficiency, cover up the printed data and see if the chart still works.

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A key decision for the designer is the relative importance of (a) the number of projects reaching Phase III, versus (b) the number of projects utilizing specific vaccine strategies.

This next chart emphasizes the clinical phases:

 

Contrast this with the version shown in the online edition of Bloomberg (link), which emphasizes the vaccine strategies.

If any reader can figure out the logic of the ordering of the vaccine strategies, please leave a comment below.

Deaths as percent neither of cases nor of population. Deaths as percent of normal.

Yesterday, I posted a note about excess deaths on the book blog (link). The post was inspired by a nice data visualization by the New York Times (link). This is a great example of data journalism.

Excess deaths is a superior metric for measuring the effect of Covid-19 on public health. It's better than deaths as percent of cases. Also better than percent of the population.What excess deaths measure is deaths as a percent of normal. Normal is usually defined as the average deaths in the respective week in years past.

The red areas indicate how far the deaths in the Southern states are above normal. The highest peak, registered in Texas in late July, is 60 percent above the normal level.

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The best way to appreciate the effort that went into this graphic is to imagine receiving the outputs from the model that computes excess deaths. A three-column spreadsheet with columns "state", "week number" and "estimated excess deaths".

The first issue is unequal population sizes. More populous states of course have higher death tolls. Transforming death tolls to an index pegged to the normal level solves this problem. To produce this index, we divide actual deaths by the normal level of deaths. So the spreadsheet must be augmented by two additional columns, showing the historical average deaths and actual deaths for each state for each week. Then, the excess death index can be computed.

The journalist builds a story around the migration of the coronavirus between different regions as it rages across different states  during different weeks. To this end, the designer first divides the dataset into four regions (South, West, Midwest and Northeast). Within each region, the states must be ordered. For each state, the week of peak excess deaths is identified, and the peak index is used to sort the states.

The graphic utilizes a small-multiples framework. Time occupies the horizontal axis, by convention. The vertical axis is compressed so that the states are not too distant. For the same reason, the component graphs are allowed to overlap vertically. The benefit of the tight arrangement is clearer for the Northeast as those peaks are particularly tall. The space-saving appearance reminds me of sparklines, championed by Ed Tufte.

There is one small tricky problem. In most of June, Texas suffered at least 50 percent more deaths than normal. The severity of this excess death toll is shortchanged by the low vertical height of each component graph. What forced such congestion is probably the data from the Northeast. For example, New York City:

 

New York City's death toll was almost 8 times the normal level at the start of the epidemic in the U.S. If the same vertical scale is maintained across the four regions, then the Northeastern states dwarf all else.

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One key takeaway from the graphic for the Southern states is the persistence of the red areas. In each state, for almost every week of the entire pandemic period, actual deaths have exceeded the normal level. This is strong indication that the coronavirus is not under control.

In fact, I'd like to see a second set of plots showing the cumulative excess deaths since March. The weekly graphic is better for identifying the ebb and flow while the cumulative graphic takes measure of the total impact of Covid-19.

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The above description leaves out a huge chunk of work related to computing excess deaths. I assumed the designer receives these estimates from a data scientist. See the related post in which I explain how excess deaths are estimated from statistical models.

 

Ask how you can give

A reader and colleague Georgette A was frustrated with the following graphic that appeared in the otherwise commendable article in National Geographic (link). The NatGeo article provides a history lesson on past pandemics that killed millions.

What does the design want to convey to readers?

Our attention is drawn to the larger objects, the red triangle on the left or the green triangle on the right. Regarding the red triangle, we learn that the base is the duration of the pandemic while the height of the black bar represents the total deaths.

An immediate curiosity is why a green triangle is lodged in the middle of the red triangle. Answering this question requires figuring out the horizontal layout. Where we expect axis labels we find an unexpected series of numbers (0, 16, 48, 5, 2, 4, ...). These are durations that measure the widths of the triangular bases.

To solve this puzzle, imagine the chart with the triangles removed, leaving just the black columns. Now replace the durations with index numbers, 1 to 13, corresponding to the time order of the ending years of these epidemics. In other words, there is a time axis hidden behind the chart. [As Ken reminded me on Twitter, I forgot to mention that details of each pandemic are revealed by hovering over each triangle.]

This explains why the green triangle (Antonine Plague) is sitting inside the large red triangle (Plague of Justinian). The latter's duration is 3 times that of the former, and the Antonine Plague ended before the Plague of Justinian. In fact, the Antonine occurred during 165-180 while the Justinian happened during 541-588. The overlap is an invention of the design. To receive what the design gives, we have to think of time as a sequence, not of dates.

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Now, compare the first and second red triangles. Their black columns both encode 50 million deaths. The Justinian Plague however was spread out over 48 years while the Black Death lasted just 5 years. This suggests that the Black Death was more fearsome than the Justinian Plague. And yet, the graphic presents the opposite imagery.

This is a pretty tough dataset to visualize. Here is a side-by-side bar chart that lets readers first compare deaths, and then compare durations.

In the meantime, I highly recommend the NatGeo article.

Hope and reality in one Georgia chart

Over the weekend, Georgia's State Health Department agitated a lot of people when it published the following chart:

(This might have appeared a week ago as the last date on the chart is May 9 and the title refers to "past 15 days".)

They could have avoided the embarrassment if they had read my article at DataJournalism.com (link). In that article, I lay out a set of the "unspoken conventions," things that visual designers are, or should be, doing more or less in their sleep. Under the section titled "Order", I explain the following two "rules":

• Place values in the natural order when it is available
• Retain the same order across all plots in a panel of charts

In the chart above, the natural order for the horizontal (time) axis is time running left to right. The order chosen by the designer  is roughly but not precisely decreasing height of the tallest column in each daily group. Many observers suggested that the columns were arranged to give the appearance of cases dropping over time.

Within each day, the counties are ordered in decreasing number of new cases. The title of the chart reads "number of cases over time" which sounds like cumulative cases but it's not. The "lead" changed hands so many times over the 15 days, meaning the data sequence was extremely noisy, which would be unlikely for cumulative cases. There are thousands of cases in each of these counties by May. Switching the order of the columns within each daily group defeats the purpose of placing these groups side-by-side.

Responding to the bad press, the department changed the chart design for this week's version:

This chart now conforms to the two spoken rules described above. The time axis runs left to right, and within each group of columns, the order of the counties is maintained.

The chart is still very noisy, with no apparent message.

***

Next, I'd like to draw your attention to a Data issue. Notice that the 15-day window has shifted. This revised chart runs from May 2 to May 16, which is this past Saturday. The previous chart ran from Apr 26 to May 9. 

Here's the data for May 8 and 9 placed side by side.

There is a clear time lag of reporting cases in the State of Georgia. This chart should always exclude the last few days. The case counts keep going up until it stabilizes. The same mistake occurs in the revised chart - the last two days appear as if new cases have dwindled toward zero when in fact, it reflects a lag in reporting.

The disconnect between the Question being posed and the quality of the Data available dooms this visualization. It is not possible to provide a reliable assessment of the "past 15 days" when during perhaps half of that period, the cases are under-counted.

***

This graphical distortion due to "immature" data has become very commonplace in Covid-19 graphics. It's similar to placing partial-year data next to full-year results, without calling out the partial data.

The following post from the ancient past (2005!) about a New York Times graphic shows that calling out this data problem does not actually solve it. It's a less-bad kind of thing.

The coronavirus data present more headaches for graphic designers than the financial statistics. Because of accounting regulations, we know that only the current quarter's data are immature. For Covid-19 reporting, the numbers are being adjusted for days and weeks.

Practically all immature counts are under-estimates. Over time, more cases are reported. Thus, any plots over time - if unadjusted - paint a misleading picture of declining counts. The effect of the reporting lag is predictable, having a larger impact as we run from left to right in time. Thus, even if the most recent data show a downward trend, it can eventually mean anything: down, flat or up. This is not random noise though - we know for certain of the downward bias; we just don't know the magnitude of the distortion for a while.

Another issue that concerns coronavirus reporting but not financial reporting is inconsistent standards across counties. Within a business, if one were to break out statistics by county, the analysts would naturally apply the same counting rules. For Covid-19 data, each county follows its own set of rules, not just  how to count things but also how to conduct testing, and so on.

Finally, with the politics of re-opening, I find it hard to trust the data. Reported cases are human-driven data - by changing the number of tests, by testing different mixes of people, by delaying reporting, by timing the revision of older data, by explicit manipulation, ...., the numbers can be tortured into any shape. That's why it is extremely important that the bean-counters are civil servants, and that politicians are kept away. In the current political environment, that separation between politics and statistics has been breached.

***

Why do we have low-quality data? Human decisions, frequently political decisions, adulterate the data. Epidemiologists are then forced to use the bad data, because that's what they have. Bad data lead to bad predictions and bad decisions, or if the scientists account for the low quality, predictions with high levels of uncertainty. Then, the politicians complain that predictions are wrong, or too wide-ranging to be useful. If they really cared about those predictions, they could start by being more transparent about reporting and more proactive at discovering and removing bad accounting practices. The fact that they aren't focused on improving the data gives the game away. Here's a recent post on the politics of data.

 

Twitter people UpSet with that Covid symptoms diagram

Been busy with an exciting project, which I might talk about one day. But I promised some people I'll follow up on Covid symptoms data visualization, so here it is.

After I posted about the Venn diagram used to depict self-reported Covid-19 symptoms by users of the Covid Symptom Tracker app (reported by Nature), Xan and a few others alerted me to Twitter discussion about alternative visualizations that people have made after they suffered the indignity of trying to parse the Venn diagram.

To avoid triggering post-trauma, for those want to view the Venn diagram, please click here.

[In the Twitter links below, you almost always have to scroll one message down - saving tweets, linking to tweets, etc. are all stuff I haven't fully figured out.]

Start with the Questions

Xan’s final comment is especially appropriate: "There's an over-riding Type-Q issue: count charts answer the wrong question".

As dataviz designers, we frequently get locked into the mindset of “what is the best way to present this dataset?” This line of thinking leads to overloaded graphics that attempt to answer every possible question that may arise from the data in one panoptic chart, akin to juggling 10 balls at once.

For complex datasets, it is often helpful to narrow down the list of questions, and provide a series of charts, each addressing one or two questions. I’ll come back to this point. I want to first show some of the nicer visuals that others have produced, which brings out the structure and complexity of this dataset.

 

The UpSet chart

The primary contender is the “UpSet” chart form, as best exemplified by Bart’s effort

The centerpiece of this chart is the matrix of dots. The horizontal rows of dots represent the presence of specific symptoms such as cough and anosmia (loss of smell and taste). The vertical columns are intuitive, once you get it. They represent combinations of symptoms, and the fill/no-fill of the dots indicates which symptoms are being combined. For example, the first column counts people reporting fatigue plus anosmia (but nothing else).

The UpSet chart clearly communicates the structure of the data. In many survey questions (including this one conducted by the Symptom Tracker app), respondents are allowed to check/tick more than one answer choices. This creates a situation where the number of answers (here, symptoms) per respondent can be zero up to the total number of answer choices.

So far, we have built a structure like we have drawn country outlines on a map. There is no data yet. The data are primarily found in the sidebar histograms (column/bar charts). Reading horizontally to the right side, one learns that the most frequently reported symptom was fatigue, covering 88 percent of the users.* Reading vertically, one learns that the top combination of symptoms was fatigue plus anosmia, covering 16 percent of users.

***

Now come the divisive acts.

Act 1: Bart orders the columns in a particular way that meets his subjective view of how he wants readers to see the data. The columns are sorted from the most frequent combinations to the least. The histogram has a “long tail”, with most of the combinations receiving a small proportion of the total. The top five combinations is where the bulk of the data is – I’d have liked to see all five columns labeled, without decimal places.

This is a choice on the part of the designer. Nils, for example, made two versions of his UpSet charts. The second version arranges the combinations from singles to quintuples.

 

Digression: The Visual in Data Visualization

The two rendering of “UpSet” charts, by Nils and Bart, is a perfect illustration of the Trifecta Checkup framework. Each corner of the Trifecta is an independent dimension, and yet all must sync. With the same data and the same question types, what differentiates the two versions is the visual design.

See how many differences you can find, and make your own design choices!

 

I place the digression here because Act 1 above has to do with the Q corner, and both visual designs can accommodate the sorting decisions. But Act 2 below pertains to the V corner.

Act 2: Bart applies a blue gradient to the matrix of dots that reinforces his subjective view about identifying frequent combinations of symptoms. Nils, by contrast, uses the matrix to show present/absent only.

I’m not sure about Act 2. I think the addition of the color gradient overloads the matrix in the chart. It has the nice effect of focusing the reader’s attention on the top 5 combinations but it also requires the reader to have understood the meaning of columns first. Perhaps applying the gradient to the histogram up top rather than the dots in the matrix can achieve the same goal with less confusion.

 

Getting Obtuse

For example, some readers (e.g. Robin) expressed confusion.

Robin is alleging something the chart doesn’t do. He pointed out (correctly) that while 16 percent experienced fatigue and anosmia only (without other symptoms), more than 50 percent reported fatigue and anosmia, plus other symptoms. That nugget of information is deeply buried inside Bart’s chart – it’s the sum of each column for which the first two dots are filled in. For example, the second column represents fatigue+anosmia+cough. So Robin wants to aggregate those up.

Robin’s critique arises from the Q(uestion) corner. If the designer wants to highlight specific combinations that occur most frequently in the data, then Bart’s encoding makes perfect sense. On the other hand, if the purpose is to highlight pairs of symptoms that occur most frequently together (disregarding symptoms outside each pair), then the data must be further aggregated. The switch in the Question requires more Data manipulation, which then affects the Visualization. That's the essence of the Trifecta Checkup framework.

Rest assured, the version that addresses Robin’s point will not give an easy answer to Bart’s question. In fact, Xan whipped up a bar chart in response:

This is actually hard to comprehend because Robin’s question is even hard to state. The first bar shows 87 percent of users reported fatigue as a symptom, the same number that appeared on Bart’s version on the right side. Then, the darkened section of the bar indicates the proportion of users who reported only fatigue and nothing else, which appears to be about 10 percent. So 1 out of 9 reported just fatigue while 8 out of 9 who reported fatigue also experienced other symptoms.

 

Xan’s bar chart can be flipped 90 degrees and replace Bart’s histogram on top of the matrix. But you see, we end up with the same problem as I mentioned up top. By jamming more insights from more questions onto the same chart, we risk dropping the other balls that were already in the air.

So, my advice is always to first winnow down the list of questions you want to address. And don’t be afraid of making a series of charts instead of one panoptic chart.

***

Act 3: Bart decides to leave out labels for the columns.

This is a curious choice given the key storyline we’ve been working with so far (the Top 5 combinations of symptoms). But notice how annoying this problem is. Combinations require long text, which must be written vertically or slanted on this design. Transposing could help but not really. It’s just a limitation of this chart form. For me, reading the filled dots underneath the columns as column labels isn’t a show-stopper.

 

Histograms vs Bar Charts

It’s worth pointing out that the sidebar “histograms” are not both histograms. I tend to think of histograms as a specific type of bar (column) chart, in which the sum of the bars (columns) can be interpreted as a whole. So all histograms are bar charts but only some bar charts are histograms.

The column chart up top is a histogram. The combinations of symptoms are disjoint, and the total of the combinations should be the total number of answer choices selected by all respondents. The bar chart on the right side however is not a histogram. Each percentage is a proportion to the whole, and adding those percentages yields way above 100%.

I like the annotation on Bart’s chart a lot. They are succinct and they give just the right information to explain how to read the chart.

 

Limitations

I already mentioned the vertical labeling issue for UpSet charts. Here are two other considerations for you.

The majority of the plotting area is dedicated to the matrix of dots. The matrix contains merely labels for data. They are like country boundaries on a map. While it lays out the structure of data very clearly, the designer should ask whether it is essential for the readers to see the entire landscape.

In real-world data, the “long tail” phenomenon we saw earlier is very common. With six featured symptoms, there are 2^6 = 64 possible combinations of symptoms (minus 1 if they filtered out those not reporting symptoms*), almost all of which will be empty. Should the low-frequency columns be removed? This is not as controversial as you think, because implicitly both Bart and Nils already dropped all empty combinations!

 

Data and Code

Kieran Healy left a comment on the last post, and you can find both the data (thank you!) and some R code for UpSet charts at his blog.

Also, Nils has a Shiny app on Github.

 

(*) One must be very careful about what “users” are being represented. They form a tiny subset of users of the Symptom Tracker app, just those who have previously taken a diagnostic test and have self-reported at least one symptom. I have separately commented on the analyses of this dataset by the team behind the app. The first post discusses their analytical methods, the second post examines how they pre-processed the data, and a future post will describe the data collection practices. For the purpose of this blog post, I’ll ignore any data issues.

(#) Bart’s chart is conceptual because some of the columns of dots are repeated, and there is one column without fills, which should have been removed by a pre-processing step applied by the research team.

Make your color legend better with one simple rule

The pie chart about COVID-19 worries illustrates why we should follow a basic rule of constructing color legends: order the categories in the way you expect readers to encounter them.

Here is the chart that I discussed the other day, with the data removed since they are not of concern in this post. (link)

First look at the pie chart. Like me, you probably looked at the orange or the yellow slice first, then we move clockwise around the pie.

Notice that the legend leads with the red square ("Getting It"), which is likely the last item you'll see on the chart.

This is the same chart with the legend re-ordered:

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Simple charts can be made better if we follow basic rules of construction. When used frequently, these rules can be made silent. I cover rules for legends as well as many other rules in this Long Read article titled "The Unspoken Conventions of Data Visualization" (link).

Pie chart conventions

I came across this pie chart from a presentation at an industry meeting some weeks ago:

This example breaks a number of the unspoken conventions on making pie charts and so it is harder to read than usual.

Notice that the biggest slice starts around 8 o'clock, and the slices are ordered alphabetically by the label, rather than numerically by size of the slice.

The following is the same chart ordered in a more conventional way. The largest slice is placed along the top vertical, and the other slices are arranged in a clock-wise manner from larger to smaller.

This version is easier to read because the reader does not need to think about the order of the slices. The expectation of decreasing size is met.

The above pie chart, though, reveals breaking of another convention. The colors on this chart signify nothing! The general rule is color differences should encode data differences. Here, the colors should go from deepest to lightest. (One can even argue that different tinges is redundant.)

You see how this version is even better. In the previous version, the colors are distracting. You're wondering what they mean, and then you realize they signify nothing.

***

As designers of graphics, we follow a bunch of conventions silently. When a design deviates from it, it's harder to understand.

Recently, I wrote a long article for DataJournalism.com, setting out many of these unspoken conventions. Read it here.

 

Gazing at petals

Reader Murphy pointed me to the following infographic developed by Altmetric to explain their analytics of citations of journal papers. These metrics are alternative in that they arise from non-academic media sources, such as news outlets, blogs, twitter, and reddit.

The key graphic is the petal diagram with a number in the middle.

I have a hard time thinking of this object as “data visualization”. Data visualization should visualize the data. Here, the connection between the data and the visual design is tenuous.

There are eight petals arranged around the circle. The legend below the diagram maps the color of each petal to a source of data. Red, for example, represents mentions in news outlets, and green represents mentions in videos.

Each petal is the same size, even though the counts given below differ. So, the petals are like a duplicative legend.

The order of the colors around the circle does not align with its order in the table below, for a mysterious reason.

Then comes another puzzle. The bluish-gray petal appears three times in the diagram. This color is mapped to tweets. Does the number of petals represent the much higher counts of tweets compared to other mentions?

To confirm, I pulled up the graphic for a different paper.

Here, each petal has a different color. Eight petals, eight colors. The count of tweets is still much larger than the frequencies of the other sources. So, the rule of construction appears to be one petal for each relevant data source, and if the total number of data sources fall below eight, then let Twitter claim all the unclaimed petals.

A third sample paper confirms this rule:

None of the places we were hoping to find data – size of petals, color of petals, number of petals – actually contain any data. Anything the reader wants to learn can be directly read. The “score” that reflects the aggregate “importance” of the corresponding paper is found at the center of the circle. The legend provides the raw data.

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Some years ago, one of my NYU students worked on a project relating to paper citations. He eventually presented the work at a conference. I featured it previously.

Notice how the visual design provides context for interpretation – by placing each paper/researcher among its peers, and by using a relative scale (percentiles).

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I’m ignoring the D corner of the Trifecta Checkup in this post. For any visualization to be meaningful, the data must be meaningful. The type of counting used by Altmetric treats every tweet, every mention, etc. as a tally, making everything worth the same. A mention on CNN counts as much as a mention by a pseudonymous redditor. A pan is the same as a rave. Let’s not forget the fake data menace (link), which  affects all performance metrics.

Bubble charts, ratios and proportionality

A recent article in the Wall Street Journal about a challenger to the dominant weedkiller, Roundup, contains a nice selection of graphics. (Dicamba is the up-and-comer.)

The change in usage of three brands of weedkillers is rendered as a small-multiples of choropleth maps. This graphic displays geographical and time changes simultaneously.

The staircase chart shows weeds have become resistant to Roundup over time. This is considered a weakness in the Roundup business.

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In this post, my focus is on the chart at the bottom, which shows complaints about Dicamba by state in 2019. This is a bubble chart, with the bubbles sorted along the horizontal axis by the acreage of farmland by state.

Below left is a more standard version of such a chart, in which the bubbles are allowed to overlap. (I only included the bubbles that were labeled in the original chart).

The WSJ’s twist is to use the vertical spacing to avoid overlapping bubbles. The vertical axis serves a design perogative and does not encode data.  

I’m going to stick with the more traditional overlapping bubbles here – I’m getting to a different matter.

***

The question being addressed by this chart is: which states have the most serious Dicamba problem, as revealed by the frequency of complaints? The designer recognizes that the amount of farmland matters. One should expect the more acres, the more complaints.

Let's consider computing directly the number of complaints per million acres.

The resulting chart (shown below right) – while retaining the design – gives a wholly different feeling. Arkansas now owns the largest bubble even though it has the least acreage among the included states. The huge Illinois bubble is still large but is no longer a loner.

Now return to the original design for a moment (the chart on the left). In theory, this should work in the following manner: if complaints grow purely as a function of acreage, then the bubbles should grow proportionally from left to right. The trouble is that proportional areas are not as easily detected as proportional lengths.

The pair of charts below depict made-up data in which all states have 30 complaints for each million acres of farmland. It’s not intuitive that the bubbles on the left chart are growing proportionally.

Now if you look at the right chart, which shows the relative metric of complaints per million acres, it’s impossible not to notice that all bubbles are the same size.

Taking small steps to bring out the message

Happy new year! Good luck and best wishes!

***

We'll start 2020 with something lighter. On a recent flight, I saw a chart in The Economist that shows the proportion of operating income derived from overseas markets by major grocery chains - the headline said that some of these chains are withdrawing from international markets.

The designer used one color for each grocery chain, and two shades within each color. The legend describes the shades as "total" and "of which: overseas". As with all stacked bar charts, it's a bit confusing where to find the data. The "total" is actually the entire bar, not just the darker shaded part. The darker shaded part is better labeled "home market" as shown below:

The designer's instinct to bring out the importance of international markets to each company's income is well placed. A second small edit helps: plot the international income amounts first, so they line up with the vertical zero axis. Like this:

This is essentially the same chart. The order of international and home market is reversed. I also reversed the shading, so that the international share of income is displayed darker. This shading draws the readers' attention to the key message of the chart.

A stacked bar chart of the absolute dollar amounts is not ideal for showing proportions, because each bar is a different length. Sometimes, plotting relative values summing to 100% for each company may work better.

As it stands, the chart above calls attention to a different message: that Walmart dwarfs the other three global chains. Just the international income of Walmart is larger than the total income of Costco.

***

Please comment below or write me directly if you have ideas for this blog as we enter a new decade. What do you want to see more of? less of?