7 ms·

The misuse of colour in science communication

155 points by fluctuation 6y ago

eggsnbacon1 6y ago
50% of graphics would be 100% better if we banned red/green color schemes and pie charts
jjgreen 6y ago
Most of the colour-ramps mentioned in this article can be found in several formats at cpt-city: http://soliton.vm.bytemark.co.uk/pub/cpt-city/ http://soliton.vm.bytemark.co.uk/pub/cpt-city/
- fluctuation 6y ago
  Excellent site! Thank you.
- supernova87a 6y ago
  This is what the article was missing -- real examples that you can see how to implement and why the differences help!
epistasis 6y ago
This is really fantastic to see, and I hope it is read widely. Anything that can get rid of jet is a godsend for better figures. My only minor quibble is the use of "scientifically" in phrases like "scientifically derived color maps." Since there's no general "scienctific" concept, and it's actually about the color values perceptual consistency, using a term that reflects that specific "scientific" aspect would be a lot clearer. The terms "scientific" and "unscientific" are highly subjective and do not convey much useful meaning, IMHO. And when an article is read by non-scientists, which I hope this article will be, using terms like "unscientific" reinforces the false popular perception that scientists are commonly dividing the world into "scientific" and "unscientific" like a 1950s Time magazine article. But again, very minor quibble in what is a very important message.
blix 6y ago
This is a weird article. Jet is effectively a divergent colormap and allows highlighting of extemes, but none of the other colormaps they consider are useful in this context. Jet isn't competing with batlow and viridis, it's competing with BwR. Yeah batlow looks better than jet on a photograph, but that doesn't mean it's necessarily better for communicating data that doesn't share the underlying features of photographs. I'd like to see whether jet or batlow has better accuracy when asking readers to eyeball data values from -1 to 1 based on color. I personally avoid jet etc, but the motivations they give here seem to miss the point of why these colormaps are used.
- deleted 6y ago
  [deleted]
- rozab 6y ago
  I have rarely seen Jet used as a divergent colourmap (i.e. in places where the data is roughly centred around 0), and it would do a particularly poor job at this. There are two perceptual peaks in lightness, in the cyan and yellow sections, and neither of these are centred. Even worse, you can can see in the visualisation of various types of colourblindness that with protanopia only the cyan peak is visible, and with tritanopia only the yellow peak is visible.
  - blix 6y ago
    If your data is centered around zero (i.e. lots of uninteresting data points near zero), why would you want your perceptual peak there? I can't think of any divergent colormap that has this feature. In jet the cyan and yellow regions highlight small deviations from zero, which are usually more interesting than zero itself. I understand that jet is poor for accessiblity, and I don't use it for that reason, but in my experience jet is used frequently for divergent data and highlighting extreme values. The article's argument for perceptually uniform colormaps in this context is weak to non-existent. Surely roma wouldn't look very good on a photo of Curie.
    - nemetroid 6y ago
KingOfCoders 6y ago
I hate it when climate pictures just make the highest temperatures bright red. Because using the emotional response to colors is not scientific. It just makes science look like propaganda.
- ponderingfish 6y ago
  Why? [Trying to learn more about your train of thought]
  - hombre_fatal 6y ago
    "Why" isn't such an obscure question that you need to explain what it means.
- garden_hermit 6y ago
  With temperatures, the blue-red color-map is makes intuitive sense because, culturally, we already have an association of blue = cold and red = hot. The issue though is where to draw the center between blue and red? Like, when do we transition from light blue to light red? The average temperature? the freezing point? And even then, what color goes in the middle? White, grey, and black are common, but not necessarily natural or perfect options. One solution is to use a sequential, non-diverging color map that starts at white/light red, and gets more red with higher temperature (or blue, or green). But then we miss out on that intuitive blue/red relationship, and people may have a hard time interpreting "light red" as a low, cold temperature.
  - SubiculumCode 6y ago
    green goes in the middle...at least in a few colormaps I've seen...oh wait...that's Jet.
sthnblllII 6y ago
> [scientists] fail to condemn the proliferation among themselves if I don't think scientists should condemn one another for their choice of colors in graphs. Make your argument for one set of colors vs another and scientists can decide for themselves if they agree.
SubiculumCode 6y ago
Anything that can help me think less about colormaps when producing figures is a clear plus. I've actually started to prefer grayscale figures for this reason.
- _Wintermute 6y ago
  This is what really confused me when they showed the black and white image as the ground-truth in Fig.1, so what exactly is the batlow colour map adding in this example?
kzrdude 6y ago
Nice to see this again, but the viridis colormap and the related talks were spread widely a few years ago. What does the Nature article mean now, is the publishing process really this slow?
yiyus 6y ago
The jet colormap is horrible, I hate it with a passion, and I know its deficiencies when compared with properly designed colormaps. But I use it all the time. In certain fields (eg FEM applied to mechanical engineering), it's just one of those absolutely counterproductive standards we have to deal with all the time. Sometimes I have tried using side-by-side figures with other colormap, usually to prove some specific point, but changing the habits of a whole field is really difficult. It is even more difficult when there is not a clear alternative, but several to choose from; I have seen a few other people using alternative colormaps too and they did not use the same as me (or I did not use the same as them). To give a more extreme example: if a doctor has to check my cancer tests and he has been diagnosing tumors using the jet colormap for decades, I would not feel comfortable if my results were given to him using the much better cividis colormap.
- johnminter 6y ago
  That is why many prefer viridis.
  - yiyus 6y ago
    What do you mean by "that"?
hoseja 6y ago
They go too far in the other direction in catering to all possible colorblindnesses. They seem bland and not much different from grayscale. Give me a perception-corrected rainbow, not these two color slimy things.
unemphysbro 6y ago
I'd like to add that figure design should be colorblind friendly. I think anyone that presents data should read this article: https://jfly.uni-koeln.de/color/ https://jfly.uni-koeln.de/color/
RiversHaveWings 6y ago
I found a matplotlib-compatible implementation of these colormaps here (under the 'scientific' submodule): https://jiffyclub.github.io/palettable/ https://jiffyclub.github.io/palettable/
s1mon 6y ago
The first thing I did when I opened the article was to search for viridis. It is in there, but in a sidebar. As others have pointed out, it's weird to make such a big deal about the same sort of thinking which has been done quite well previously, and then bury it in your notes.
- s1mon 6y ago
  If you haven't already watched this, here's the SciPy2015 presentation on the development of viridis. It helps to explain the importance of color maps and how human visual color perception works. https://www.youtube.com/watch?v=xAoljeRJ3lU https://www.youtube.com/watch?v=xAoljeRJ3lU
bluenose69 6y ago
I'm not entirely sure how this got past the Nature editors, since a lot of this is old hat, having been discussed widely, and for many years. The message is fine, as far as it goes. However, I would argue that perceptual neutrality is not the only measure of a colour scale. I hate jet as much as the next person, but I still do use the similar turbo scheme (which is less 'jagged' in perceptual space) when I teach. Why? Because it lets me show an image of a complex field (perhaps sea-surface temperature) and point to a spot of some value, and ask students to visually trace nearby spots of the same hue. It doesn't really matter if some students perceive the same hue for two different actual hues. So long as the neighbouring hues differ, the students can trace a local contour. I need that to explain certain topics. Using a colour scheme with just a couple of hues makes it very, very, difficult to trace contours. It's even worse when an image is projected onto a screen, in a classroom or at a meeting. Speaker: "See this slightly yellowish green on the colourbar, at 10C? Where is it in the map?" Audience: "I dunno, when's the next coffee break?" Essentially, colour maps with a lot of hues can make images into something like a contour diagram. This can help, because some fields are so ragged that contours are difficult to understand. Sometimes, a linear mapping between data values and the perceived colour is the end goal. Other times, not.
- twic 6y ago
  There's a kind of colourmap which is a luminance gradient in a single hue, repeated over and over again with different hues. See the various "ramps" colourmaps in ImageJ (where colourmaps are called "look-up tables", or LUTs): http://soliton.vm.bytemark.co.uk/pub/cpt-city/imagej/index.html http://soliton.vm.bytemark.co.uk/pub/cpt-city/imagej/index.h... I've seen it with a single hue as well. This kind of colourmap makes it really easy to see contours. The tradeoff is that it's hard to make comparisons between distant areas of the image.
  - bluenose69 6y ago
    Thanks. Yes, I like that type, and use it sometimes. I tend to use light-to-dark brown hues, which can give a pleasing wood-grain effect.
- 6y ago
splittingTimes 6y ago
IBM did research back in the 90s on perceptually-based colormaps and how to best represent various types of data within the color dimensions of luminescence, saturation and hue [1]. For exmpale, they found that, (1) Hue was not a good dimension for encoding magnitude information, i.e. rainbow color maps are bad. (2) The mechanisms in human vision responsible for high spatial frequency information processing are luminance channels. If the data to be represented have high spatial frequency, use a colormap which has a strong luminance variation across the data range. (3) For interval and ratio data, both luminance- and saturation-varying colormaps should produce the effect of having equal steps in data value correspond to equal perceptual steps, but the first will be most effective for high spatial frequency data variations and the second will be most effective for low spatial frequency variations. === [1] https://www.research.ibm.com/people/l/lloydt/color/color.HTM https://www.research.ibm.com/people/l/lloydt/color/color.HTM or as pdf: https://github.com/frankMilde/interesting-reads/blob/master/ibm-research__why-should-engineers-and-scientists-be-worried-about-color.pdf https://github.com/frankMilde/interesting-reads/blob/master/...
- swimfar 6y ago
  "rainbow color maps are bad" I disagree with blanket statements like this. Rainbow color maps aren't ideal for showing relative difference in values. But they are great if you want to be able to tell what the value (range) in a given location is. This is almost impossible with a 10-shade grey-scale legend or a height map. Disclaimer: I use rainbow color maps all the time because I'm often interested in critical value areas of my plots.
  - username90 6y ago
    Color blind people likely wont be able to read your rainbow plots though. For example, for me Jet is just Blue - White - Green - Dark Green, with white being left of the middle. (Blue + Green is white since I don't see red) So for me reading a Jet plot is basically impossible, they just doesn't make sense. Like, if a value is weak it is the brightest white, then if it gets even lower it gets blue. It peaks at green in the middle and then goes darker and darker as it gets stronger. Totally unintuitive. Edit: Even worse is that how I see it depends strongly on what medium you use for the red and green channels. On some screens/paints red is basically black while others are almost fully green, depending on exactly where in the spectrum it is.
hwc 6y ago
See also ”Rainbow Color Map (Still) Considered Harmful” from 2007.

155 points by fluctuation 6y ago

50% of graphics would be 100% better if we banned red/green color schemes and pie charts

Most of the colour-ramps mentioned in this article can be found in several formats at cpt-city: http://soliton.vm.bytemark.co.uk/pub/cpt-city/ http://soliton.vm.bytemark.co.uk/pub/cpt-city/

fluctuation 6y ago
Excellent site! Thank you.
supernova87a 6y ago
This is what the article was missing -- real examples that you can see how to implement and why the differences help!

epistasis 6y ago

This is really fantastic to see, and I hope it is read widely. Anything that can get rid of jet is a godsend for better figures. My only minor quibble is the use of "scientifically" in phrases like "scientifically derived color maps." Since there's no general "scienctific" concept, and it's actually about the color values perceptual consistency, using a term that reflects that specific "scientific" aspect would be a lot clearer. The terms "scientific" and "unscientific" are highly subjective and do not convey much useful meaning, IMHO. And when an article is read by non-scientists, which I hope this article will be, using terms like "unscientific" reinforces the false popular perception that scientists are commonly dividing the world into "scientific" and "unscientific" like a 1950s Time magazine article. But again, very minor quibble in what is a very important message.

blix 6y ago

This is a weird article. Jet is effectively a divergent colormap and allows highlighting of extemes, but none of the other colormaps they consider are useful in this context. Jet isn't competing with batlow and viridis, it's competing with BwR. Yeah batlow looks better than jet on a photograph, but that doesn't mean it's necessarily better for communicating data that doesn't share the underlying features of photographs. I'd like to see whether jet or batlow has better accuracy when asking readers to eyeball data values from -1 to 1 based on color. I personally avoid jet etc, but the motivations they give here seem to miss the point of why these colormaps are used.

deleted 6y ago
[deleted]
rozab 6y ago
I have rarely seen Jet used as a divergent colourmap (i.e. in places where the data is roughly centred around 0), and it would do a particularly poor job at this. There are two perceptual peaks in lightness, in the cyan and yellow sections, and neither of these are centred. Even worse, you can can see in the visualisation of various types of colourblindness that with protanopia only the cyan peak is visible, and with tritanopia only the yellow peak is visible.
- blix 6y ago
  If your data is centered around zero (i.e. lots of uninteresting data points near zero), why would you want your perceptual peak there? I can't think of any divergent colormap that has this feature. In jet the cyan and yellow regions highlight small deviations from zero, which are usually more interesting than zero itself. I understand that jet is poor for accessiblity, and I don't use it for that reason, but in my experience jet is used frequently for divergent data and highlighting extreme values. The article's argument for perceptually uniform colormaps in this context is weak to non-existent. Surely roma wouldn't look very good on a photo of Curie.
  - nemetroid 6y ago

KingOfCoders 6y ago

I hate it when climate pictures just make the highest temperatures bright red. Because using the emotional response to colors is not scientific. It just makes science look like propaganda.

ponderingfish 6y ago
Why? [Trying to learn more about your train of thought]
- hombre_fatal 6y ago
  "Why" isn't such an obscure question that you need to explain what it means.
garden_hermit 6y ago
With temperatures, the blue-red color-map is makes intuitive sense because, culturally, we already have an association of blue = cold and red = hot. The issue though is where to draw the center between blue and red? Like, when do we transition from light blue to light red? The average temperature? the freezing point? And even then, what color goes in the middle? White, grey, and black are common, but not necessarily natural or perfect options. One solution is to use a sequential, non-diverging color map that starts at white/light red, and gets more red with higher temperature (or blue, or green). But then we miss out on that intuitive blue/red relationship, and people may have a hard time interpreting "light red" as a low, cold temperature.
- SubiculumCode 6y ago
  green goes in the middle...at least in a few colormaps I've seen...oh wait...that's Jet.

sthnblllII 6y ago

> [scientists] fail to condemn the proliferation among themselves if I don't think scientists should condemn one another for their choice of colors in graphs. Make your argument for one set of colors vs another and scientists can decide for themselves if they agree.

SubiculumCode 6y ago

Anything that can help me think less about colormaps when producing figures is a clear plus. I've actually started to prefer grayscale figures for this reason.

_Wintermute 6y ago
This is what really confused me when they showed the black and white image as the ground-truth in Fig.1, so what exactly is the batlow colour map adding in this example?

kzrdude 6y ago

Nice to see this again, but the viridis colormap and the related talks were spread widely a few years ago. What does the Nature article mean now, is the publishing process really this slow?

yiyus 6y ago

The jet colormap is horrible, I hate it with a passion, and I know its deficiencies when compared with properly designed colormaps. But I use it all the time. In certain fields (eg FEM applied to mechanical engineering), it's just one of those absolutely counterproductive standards we have to deal with all the time. Sometimes I have tried using side-by-side figures with other colormap, usually to prove some specific point, but changing the habits of a whole field is really difficult. It is even more difficult when there is not a clear alternative, but several to choose from; I have seen a few other people using alternative colormaps too and they did not use the same as me (or I did not use the same as them). To give a more extreme example: if a doctor has to check my cancer tests and he has been diagnosing tumors using the jet colormap for decades, I would not feel comfortable if my results were given to him using the much better cividis colormap.

johnminter 6y ago
That is why many prefer viridis.
- yiyus 6y ago
  What do you mean by "that"?

hoseja 6y ago

They go too far in the other direction in catering to all possible colorblindnesses. They seem bland and not much different from grayscale. Give me a perception-corrected rainbow, not these two color slimy things.

unemphysbro 6y ago

I'd like to add that figure design should be colorblind friendly. I think anyone that presents data should read this article: https://jfly.uni-koeln.de/color/ https://jfly.uni-koeln.de/color/

RiversHaveWings 6y ago

I found a matplotlib-compatible implementation of these colormaps here (under the 'scientific' submodule): https://jiffyclub.github.io/palettable/ https://jiffyclub.github.io/palettable/

s1mon 6y ago

The first thing I did when I opened the article was to search for viridis. It is in there, but in a sidebar. As others have pointed out, it's weird to make such a big deal about the same sort of thinking which has been done quite well previously, and then bury it in your notes.

s1mon 6y ago
If you haven't already watched this, here's the SciPy2015 presentation on the development of viridis. It helps to explain the importance of color maps and how human visual color perception works. https://www.youtube.com/watch?v=xAoljeRJ3lU https://www.youtube.com/watch?v=xAoljeRJ3lU

bluenose69 6y ago

I'm not entirely sure how this got past the Nature editors, since a lot of this is old hat, having been discussed widely, and for many years. The message is fine, as far as it goes. However, I would argue that perceptual neutrality is not the only measure of a colour scale. I hate jet as much as the next person, but I still do use the similar turbo scheme (which is less 'jagged' in perceptual space) when I teach. Why? Because it lets me show an image of a complex field (perhaps sea-surface temperature) and point to a spot of some value, and ask students to visually trace nearby spots of the same hue. It doesn't really matter if some students perceive the same hue for two different actual hues. So long as the neighbouring hues differ, the students can trace a local contour. I need that to explain certain topics. Using a colour scheme with just a couple of hues makes it very, very, difficult to trace contours. It's even worse when an image is projected onto a screen, in a classroom or at a meeting. Speaker: "See this slightly yellowish green on the colourbar, at 10C? Where is it in the map?" Audience: "I dunno, when's the next coffee break?" Essentially, colour maps with a lot of hues can make images into something like a contour diagram. This can help, because some fields are so ragged that contours are difficult to understand. Sometimes, a linear mapping between data values and the perceived colour is the end goal. Other times, not.

twic 6y ago
There's a kind of colourmap which is a luminance gradient in a single hue, repeated over and over again with different hues. See the various "ramps" colourmaps in ImageJ (where colourmaps are called "look-up tables", or LUTs): http://soliton.vm.bytemark.co.uk/pub/cpt-city/imagej/index.html http://soliton.vm.bytemark.co.uk/pub/cpt-city/imagej/index.h... I've seen it with a single hue as well. This kind of colourmap makes it really easy to see contours. The tradeoff is that it's hard to make comparisons between distant areas of the image.
- bluenose69 6y ago
  Thanks. Yes, I like that type, and use it sometimes. I tend to use light-to-dark brown hues, which can give a pleasing wood-grain effect.
6y ago

splittingTimes 6y ago

IBM did research back in the 90s on perceptually-based colormaps and how to best represent various types of data within the color dimensions of luminescence, saturation and hue [1]. For exmpale, they found that, (1) Hue was not a good dimension for encoding magnitude information, i.e. rainbow color maps are bad. (2) The mechanisms in human vision responsible for high spatial frequency information processing are luminance channels. If the data to be represented have high spatial frequency, use a colormap which has a strong luminance variation across the data range. (3) For interval and ratio data, both luminance- and saturation-varying colormaps should produce the effect of having equal steps in data value correspond to equal perceptual steps, but the first will be most effective for high spatial frequency data variations and the second will be most effective for low spatial frequency variations. === [1] https://www.research.ibm.com/people/l/lloydt/color/color.HTM https://www.research.ibm.com/people/l/lloydt/color/color.HTM or as pdf: https://github.com/frankMilde/interesting-reads/blob/master/ibm-research__why-should-engineers-and-scientists-be-worried-about-color.pdf https://github.com/frankMilde/interesting-reads/blob/master/...

swimfar 6y ago
"rainbow color maps are bad" I disagree with blanket statements like this. Rainbow color maps aren't ideal for showing relative difference in values. But they are great if you want to be able to tell what the value (range) in a given location is. This is almost impossible with a 10-shade grey-scale legend or a height map. Disclaimer: I use rainbow color maps all the time because I'm often interested in critical value areas of my plots.
- username90 6y ago
  Color blind people likely wont be able to read your rainbow plots though. For example, for me Jet is just Blue - White - Green - Dark Green, with white being left of the middle. (Blue + Green is white since I don't see red) So for me reading a Jet plot is basically impossible, they just doesn't make sense. Like, if a value is weak it is the brightest white, then if it gets even lower it gets blue. It peaks at green in the middle and then goes darker and darker as it gets stronger. Totally unintuitive. Edit: Even worse is that how I see it depends strongly on what medium you use for the red and green channels. On some screens/paints red is basically black while others are almost fully green, depending on exactly where in the spectrum it is.

hwc 6y ago

See also ”Rainbow Color Map (Still) Considered Harmful” from 2007.