Q57 - Phase 3 collection map figure

[cclarkson]

Hi @hardingnj, @leehart, @alimanfoo

I've build three rough versions of the first panel (Western) to allow further discussion. Mali still needs some fine tuning, but you get the idea. "Western" is by far the most complex panel and if we can get something that works here, it will be fine for the other two.

• no pie scale.
• no country labels
• with pie scale

Things to discuss here include:

• placement of <10 sites, e.g. the zorder, colour?
• country labels are difficult to place in "Western", see Guinea-Bissau, ideas for best way of indicating country? Currently I fear the labels could mislead.
• scaling of pies, keep or ditch?

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[leehart]

I think the country labels are OK actually. I would say The Gambia is the most ambiguous, but I don't think there's any real risk of a problem (confusion with Senegal or Mauritania).

I think using red circles for the sites might be a slight problem since red (of a different hue) is already being used to convey information about species.

Another visual problem with the site dots might be that it looks a bit like some of the pies are originating from those particular sites, or very close to, which might be confusing. I don't have a solution though.

I agree that the z-index of the site dots is an puzzle. It looks rough when they appear beneath the origin lines, but it will look odd if they appear above the origin lines or pies too.

I wonder if small green asterisks [Or maybe simple squares?] for the site locations would be better, to help distinguish them from the pies. It's not uncommon to see symbols on maps to indicate a type of site. (Don't use a cross!)

The scaled pies don't look too bad to me, and would counter the question "Why didn't you scale the pies to indicate sample size?".

I don't like the way the borders are thinner where the pies collide in Burkina Faso. I would also adjust the position of the Cote d'Ivoire pie so that it's clear that the origin line belongs to the pie, because it currently intersects with the land border.

The black borders and origin lines of the pies might stand out better if the black keyline of the map (land border) was slightly lighter, i.e. dark grey.

The text would probably look better if it had a white glow rather than a white box, but that might be asking too much! I'd be happy to look into that, but I suspect these map APIs are more difficult/restricted than the web-based APIs I've worked with.

It might look better if the pie's origin-lines taper to a point, like a pin or needle, rather than being just a simple line, but again that's just aesthetic polishing. It might make it clearer that it's pointing to a place on the map, rather than something else, like the country label. But it might not be worth the time investment.

[cclarkson]

Adds legends

• no scaling pies - legend placement here is rough
• scaled pies

[hardingnj]

Thanks Chris- looking great!

• I think it looks better without the country labels.
• Agree with Lee, re the individual samples. Black squares would be a good fit I think.
• I think the squares have to appear below pies, but above everything else
• Like the scaling- I think that works

The black borders and origin lines of the pies might stand out better if the black keyline of the map (land border) was slightly lighter, i.e. dark grey.

Agree if possible

It might look better if the pie's origin-lines taper to a point, like a pin or needle, rather than being just a simple line, but again that's just aesthetic polishing. It might make it clearer that it's pointing to a place on the map, rather than something else, like the country label. But it might not be worth the time investment.

I think this is a nice idea... not sure how feasible it is though. A very narrow triangle maybe? Purely aesthetics though, would rather leave this for now.

[cclarkson]

Tweaks borders/outlines, <10 locations, adds full legend.

@hardingnj , @leehart - if you guys are happy with scaled pies (I think it looks cool), I will start the process of making it look neat again and apply to other regions?

Had a play with making the pie lines 'pointy', it doesn't look like there's a quick fix unfortunately. We can have 'arrows' but it looks like the overlapping points would actually be worse. As suggested, I could try plotting some kind of elongated triangles if folk think necessary?

• scaling, country labels
• scaling no labels
• no scaling, no labels

[alimanfoo]

Looking good, agree with @hardingnj. Noticed legend should be "<10" rather than ">10".

Btw any way to make the <10 markers a little smaller/less prominent?

[cclarkson]

@alimanfoo - I've made the <10 symbols smaller (and fixed the legend - thanks!). They could be reduced further or have alpha lowered a bit more, what do you think of them now?

This is now a "finished" draft for the western panel, Mali is proving quite tricky aesthetically, so I'm going to come back to it after finishing central and eastern to try a few different layouts (and, of course, tweak the other western countries' pies a bit for good luck).

[alimanfoo]

@alimanfoo - I've made the <10 symbols smaller (and fixed the legend - thanks!). They could be reduced further or have alpha lowered a bit more, what do you think of them now?

What about using a crosshair symbol (+) for the <10? Might work better in Cameroon where there will be loads of points close by?

[alimanfoo]

Central map LGTM :+1:

Labelling of countries is difficult isn't it? I'm sure many readers would benefit from having country labels. But then I think if you have labels you have to put them within the country boundaries, which causes a problem for The Gambia. I don't have any clever ideas, just talking out loud.

[hardingnj]

Sorry- missed these updates earlier! Looking great I think. The 'x's work very well. I think the western map looks better without labels. It's hard to place The Gambia and G-B correctly. I think if we do it, the labels have to be directly over the centre and we fit everything else around them.

At the moment, weak preference to go without labels though.

[leehart]

When I said "Don't use a cross!" I was concerned about using conventional map symbols for churches. Buried pirate treasure is fine by me.

I still wonder if unfilled squares would be better, so I might mock those up to have a look.

I still don't see what all the fuss is about with the country labels. Do we really expect confusion or criticism there?

I'm still curious about using a white glow instead of a box on the labels, so I might try that out for us to have a look. I might see if I can get pointier pins while I'm at it. I might play with the line thickness on the circles and pins too.

Rounded rectangles for the colour swatches is interesting. Seems to work.

The spacing between the sample size circles in the legend and their labels is a bit inconsistent. I might try to fix that.

I'd be tempted to switch the order in the sample size legend too, so that the largest circle appears first, then the whitespace for the "Sample size" heading should look more consistent with the "Species" heading, or could be adjusted accordingly.

[cclarkson]

Hi @leehart, @hardingnj, @alimanfoo,

Here's a draft of all the map panels for comments/further work.

I'm a fan of the country labels but I have both versions of each here, I feel that people can work out what the labels are trying to convey. Plus due to the size of some countries the country labels don't even fit nicely without any pies/points. I've increased the pie surround line thickness to give it more pop (toning down the borders washed out the figure a bit).

I tried unfilled squares/circles but I felt they worked less well with overplotting and had to be slightly too large for the figure to look sensible. With shape markers we need to make clear which part points to the site, e.g. with the diamonds previously, it was the bottom point which signified the site.

@leehart, tweak away, I find the legend is a pain to space nicely so it would be cool if you find an easy way to make it look nicer.

[leehart]

For the time being draft PR #16 shows the 3 maps side by side (and one way to code that), currently deployed here https://malariagen.github.io/ag1000g-phase3-data-paper/PR/16 (as HTML) and here https://malariagen.github.io/ag1000g-phase3-data-paper/PR/16/manuscript.pdf (as PDF)

I branched off this PR's branch, but my draft PR is relative to master. (I couldn't see how to change the target branch, to indicate a more explicitly nested PR, i.e. a PR-off-a-PR.)

I'm still not sure of the best way to develop or integrate this, so @cclarkson should feel free to manually copy the code (or some version of that PoC) into this branch, however suits. I will probably test out & demo some map tweaks on my draft PR Thu/Fri, but that might amount to nothing. I understand that the planned destination for this figure is the 02.results.md section currently in PR #7

[leehart]

Oh... We didn't want to orientate this figure on a landscape page, did we? (That might prove tricky.)

[alimanfoo]

Oh... We didn't want to orientate this figure on a landscape page, did we? (That might prove tricky.)

No, I think we can't have landscape pages, so everything should be designed for portrait.

[alimanfoo]

You guys are gonna hate me, but... I think we've got room to just make this a single plot. I.e., just one panel, sub-saharan Africa.

[leehart]

OK, note to self: I'll try to combine these into one map, on this PR, tomorrow.

[leehart]

• HTML https://malariagen.github.io/ag1000g-phase3-data-paper/PR/13/
• PDF https://malariagen.github.io/ag1000g-phase3-data-paper/PR/13/manuscript.pdf

[leehart]

Todo:

• [x] reposition country labels
• [x] remove test/demo figures
• [ ] ~amend figure label (?)~ [Removed.]
• [x] place figure in appropriate section (population sampling?)
• [x] consolidate notebooks into one? (remove obsolete drafts)

Anything else?

• [ ] ~make the pies a bit bigger (relatively)~ [This looks like a pain: all pies and labels would need repositioning.]
• [x] allow more space to show the Mozambique site
• [ ] grey out countries that aren't included? (Seems to require cartopy.io.shapereader.) [Requires downloading large shapefile?]
• [x] remove multi-region support in code, to simplify nb?

[alimanfoo]

Looking very nice. Couple of very minor suggestions:

• In the figure legend, suggest having n=10, n=50, n=100 instead of n=10, n=75, n=150. Just because the largest pie in the legend looks way larger than any of the pies in the actual map.
• Extend the map a little bit further south, so the Mozambique marker is not quite on the very edge.
• Font for country labels could get away with being a little smaller, which might make finding a good position a little easier?

[leehart]

I've uploaded a new version, which should be deployed to the same location, with adjusted country name positions, which have the same font size as before - I haven't tried changing that yet. This version also includes a change that extends the map to the south, already, and I also cropped the east.

I need to figure out the maths for the sample size examples in the legend, which should be simple. I'm not sure what those circle sizes are currently based on. The pie radii are sqrt(nsamples * 0.01) but the legend currently uses markersize, e.g. markersize 25 = 150 samples.

[leehart]

Sample size legend now show true sizes, and n=10, n=50, n=100.

[hardingnj]

Looking good. Thanks :) I think perhaps we could be a little more consistent with how we orient the pointer lines, ie perpendicular to the coastline where possible. Angola and Gabon look a little off. Perhaps also a case for making the lines stand out a little relative to the borders.

Let's sign this off at the meeting today!

[cclarkson]

Looks great, I'm liking the white 'glow' around the country labels. Just a couple of comments:

• maybe just a little tweaking of 'arrow' angles/pie positions (e.g. Angola, Cote d'Ivoire).
• thicken up the pie outlines and arrows to make them stand out from borders etc.

[leehart]

Ha, I purposely made the pie outlines and arrows thinner, thinking it looked better, and I actually preferred the pie outlines removed completely, except that the pie's nice shadow effect did not seem to work well at large sizes. But I will have to suffer democracy, I suppose. I didn't personally have a problem with the black lines against the geographic borders since those were switched to gray rather than black. I'll screenshot a version without the pie borders to see if that's generally preferred.

[leehart]

I think perhaps we could be a little more consistent with how we orient the pointer lines, ie perpendicular to the coastline where possible. Angola and Gabon look a little off. Perhaps also a case for making the lines stand out a little relative to the borders.

I don't understand why the pointer line orientation needs to be consistent in that way. Gabon is pointing inland because there's lots of space available there, otherwise it clashes with Bioko. Similar for Angola, where the inland orientation keeps the label away from the legend and fills up gaping space. But I can appreciate those cases might look unusual.

Any feelings on that @cclarkson ?

[leehart]

• maybe just a little tweaking of 'arrow' angles/pie positions (e.g. Angola, Cote d'Ivoire).

What is it about those that you would tweak?

• Maybe Cote d'Ivoire pie might look more organic if it wasn't straight down - maybe off to the left a little instead? [I want to put the country label a little closer. Every time I look at this, I see something else I want to tweak!]
• Do you have the same feeling about Angola as @hardingnj expresses?

[leehart]

Here's a screenshot of a version without the pie borders, for your consideration:

[leehart]

I might tone down the legend labels too. They're looking a bit too bold in that shot.

[cclarkson]

If we are now down to a myriad opinions on small features, perhaps we have the perfect plot!

Angola, yep, same as Nick, feels like it should go out to sea. Cote d'Ivoire, yep, horizontal and vertical pointers feel wrong for some reason, less organic.

As for line weights, I think that really is a personal thing. Currently I feel the figure is "muted", there's no thick black lines drawing the eye anywhere. In fact my eye is first drawn to the legend with the larger bold font and larger colour blocks. That's not a criticism at all, it makes the figure look very cohesive and perhaps that is where the eye should go first. When I've been playing with these maps recently I seem to settle on more black around pies/arrows to make them pop out a bit, as I felt that is where I wanted the viewer to concentrate.

[leehart]

I didn't have time to sort out the font styling, with Seaborn's set_context('paper'), etc., but I gather we don't want to go much bigger anyway, because the figure is already crowded, and we can't go any smaller, due to style guidelines. You can see in the screenshot below that the country labels are about the same size as the text in the figure's label, but I expect we'll need to revisit this again later. In the meantime, I'll look around for a quicker/easier tool for this task!

Let me know if I've missed anything.

[leehart]

• [x] Add the same border to the circles in the sample size legend, to help the pie sizes match by eye

[leehart]

lw=2 instead of lw=1 on the legend circles doesn't make much difference, visually. I reckon these circles should now be exactly the same footprints as the pies. One potential improvement might be to not fill the legend circles, to mitigate any silhouette effect.