A sparkline map of coviD-19 (or any name you’ll prefer)

This week-end, because of containment, I had lots of time to experiment around data and covid-19 cases, trying to figure out which graphical representation could draw the dynamics of the pandemic.

I saw a lot of graphics. The curves and their dynamics are crucial with the pandemic. Not only it is important to know what is the actual situation, but also how it was before, and how we can project ourselves to the future.

The above map is the map I made and shared on twitter :

It had quite a lot of success. It’s a mix of a line plot and a map. It gives a sense, at a single glance, of the dynamics, and looks good when animated.

After some feedback on twitter, I decied to improve the map with labels :

I only used opensource tools for it : qgis and imagemagick when animated. What’s great with opendata and open tools is that everyone can potentially integrate the data and experiment with no cost. You just have to let the ideas come, select them and find the ways to transcribe in the constrained environment of a machine : here, my computer. Somehow, the screen is my canvas painting, my mouse my brush and my keyboard my palette.

The goal of this article is to explain the method behind. It will give you a nice tutorial covering 3 qgis techniques :

  • 1-n relations
  • geometry generators
  • the use of arrays

Some next articles could get deeper into the subject with styling.

Download data

First and foremost, download the two datasets :

Here’s how the covid fr dataset looks like. It is in a long format with one row by day, unlike world John Hopskins worldwide dataset which is wide (with each column being a day)

Relation

We’ll add a relation between the departements dataset and the covid dataset. We use the department code INSEE_DEPT as a key connecting the parent table (departments layer) and the child table (covid dataset). Go to Project > Properties > Relation

Generative design

Next, go to the department layer and use a centroid symbol, but for this centroid symbol, you’ll use geometry generator to define the linestring.

As we want lines, choose line / polyline features :

And add this code in the expression (I’ll explain it just afterwards) :

with_variable(
'atlasid',
@atlas_featureid - 1,
with_variable(
'height',
100,
with_variable(
'width',
200000,
with_variable(
'nb_cas',
array_sort(
  relation_aggregate( 
    'donnees_ho_dep_DEPARTEMEN_INSEE_DEP', 
    'array_agg', 
     to_int("dc")+to_int("hosp")+to_int("rea")+to_int("rad"))
 ),
geom_from_wkt(
  'LINESTRING ('  || 
  x(centroid($geometry))||' '||y(centroid($geometry)) 
  ||','||
  array_to_string(
    array_foreach(
      generate_series(1, @atlasid), 
      -- X Coordinates
      to_string(x(centroid($geometry)) + 
      (@element/array_length(@nb_cas)*@width)) ||' '||
      -- Y coordinates
      to_string(y(centroid($geometry)) + @nb_cas[@element]*@height)
    ),
  ',') || ')'
)
))))

To understand this code, it’s important to split it into key parts. Obviously, I didn’t write it in a go. It was a trial-and-error process. Let me help you.

First, this line uses the relation we configured to store all the cases for each feature (here, each department), in an array

array_sort(
	relation_aggregate( 
		'donnees_ho_dep_DEPARTEMEN_INSEE_DEP', 
		'array_agg', 
		to_int("dc")+to_int("hosp")+to_int("rea")+to_int("rad")
	)
 )

We sort this array in ascending order of number of cases.

Note : you see the relation name being quite long, to select it, just go to the right panel and click on your relation name to put it in the code :

We store this array using the with_variable function in an array called nb_cas, to which we access with @nb_cas for future simplicity :

with_variable(
'nb_cas',
array_sort(
	relation_aggregate( 
		'donnees_ho_dep_DEPARTEMEN_INSEE_DEP', 
		'array_agg', 
		to_int("dc")+to_int("hosp")+to_int("rea")+to_int("rad")
	)
 )

Before constructing the linestring object, let’s consider this :

  • the height of the segment will be defined by the number of cases
  • and the spacing between nodes, simply, by the index of the node. One index = one node.
  • the line will start from the departement centroid

So, once we have this array of number of cases, we’ll iterate over it to get the consecutive nodes of the lines. We’ll just need the centroid coordinates, the indexes and the number of cases for each of them to build the lines

For the X coordinates of the nodes it’s this formula :

x(centroid($geometry)) + (@element/array_length(@nb_cas)*@width)

For the Y coordinates, it’s :

y(centroid($geometry)) + @nb_cas[@element]*@height

To get the index (@element), we use generate_series

generate_series(1, @atlasid), 
			-- X Coordinates
			to_string(x(centroid($geometry)) + (@element/array_length(@nb_cas)*@width)) ||' '||
			-- Y coordinates
			to_string(y(centroid($geometry)) + @nb_cas[@element]*@height)
		)

To get the number of cases, we get the array element corresponding to the index :

@nb_cas[@element]

The iteration over indexes is made with array_for_each.

array_foreach(
			generate_series(1, @atlasid), 
			-- X Coordinates
			to_string(x(centroid($geometry)) + (@element/array_length(@nb_cas)*@width)) ||' '||
			-- Y coordinates
			to_string(y(centroid($geometry)) + @nb_cas[@element]*@height)
		)

Once we have the array of coordinates, we paste them with array_to_string with the comma as delimiter, so that they can be interpreted as WKT string for a linestring

array_to_string(
		array_foreach(
			generate_series(1, @atlasid), 
			-- X Coordinates
			to_string(x(centroid($geometry)) + (@element/array_length(@nb_cas)*@width)) ||' '||
			-- Y coordinates
			to_string(y(centroid($geometry)) + @nb_cas[@element]*@height)
		),
	',')

Our final geometry, transformed from a WKT string, will be :

geom_from_wkt(
	'LINESTRING ('  || 
	x(centroid($geometry))||' '||y(centroid($geometry)) ||','||
	array_to_string(
		array_foreach(
			generate_series(1, @atlasid), 
			-- X Coordinates
			to_string(x(centroid($geometry)) + (@element/array_length(@nb_cas)*@width)) ||' '||
			-- Y coordinates
			to_string(y(centroid($geometry)) + @nb_cas[@element]*@height)
		),
	',') || ')'
)

As I said before, the first node here will be the centroid of the feature defined by its centroid. That’s why I pasted

x(centroid($geometry))||' '||y(centroid($geometry)) ||','||
	array_to_string(...

To make this the most programmatic as possible, I configured variables for the total width of the lines (@width), and the @height factor for each number of case. This way, it’s easy to change the appearance of the map

Also, I added a variable for the atlas feature id (@atlas_id) because I wanted to get the individual frames I could assemble as a GIF with ImageMagick.

For the animation, the trick consists in using an atlas and generating a series which will stop at the atlas current feature id, this one going from 0 to (n-1), n being the number of days.

So the first image will have one node (the centroid), the second one the centroid + the seconde node, the third image, the centroid + the two following nodes.

Note : why did I say 0 and (n-1) insteand of 1 and n ? It’s because the first element of an array, in qgis, is like in python : it has number 0.

That’s why my atlas_id variable has the value :

with_variable(
  'atlasid',
  @atlas_featureid - 1,
  @element
)

Maybe later I’ll write about styling the data underneath, but now, you have the mechanism and logic behind !

There’s a github repo 😉

You struggled to follow all these steps ? Wait ! I put all the project on a github repo with all the data you’ll need and a totally reproducible map. You’ll just have to follow the steps on the github page (actually, one single click on the project after downloadgin qgis)


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