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Birds of a Feather On Standards for Accessible and Interpretable Visualizations Follow up

Atul Deshpande
Postdoctoral Researcher в The Johns Hopkins University
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Birds of a Feather: On Standards for Accessible and Interpretable Visualizations - Follow Up

Atul Deshpande (Johns Hopkins University) Postdoc

Daniel Bunis (Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, 94107) Ph.D. Candidate

4:00 PM - 4:55 PM EDT on Thursday, 30 July

Community

This is a continuing discussion of the BoF that took place Monday at noon.

Moderators: Matthew McCall, Simone Bell, Erica Feick

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Atul Deshpande
Postdoctoral Researcher в The Johns Hopkins University
Daniel Bunis
Biological Data Scientist and Immunologist в University of California, San Francisco

Specialties: Signal Processing applications, Global Navigation Satellite Systems, Navigation

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Description of allowing people to unmute themselves and speak out. So yeah, I guess we can start off with a recap of what happened in the first bof quickly and then yeah. Do you want to take it from your time for the so on Monday there was an initial session that a toll had put together and we discussed visual impairments and how those sort of end up relating to looking at scientific data and our discussion covered a bunch of potential action items. But I think at all and I were both super pleasantly surprised by the number of people who came,

but it also meant that the original idea of how the meeting McDowell was not able to do it. So we figured another session today where we could go through some of the action items. What's a bit more interactive? Miss might help us actually like that a pass forward to make some of these things happen. So Best Buy are some of the ideas that either came up last time or that at all. And I had discussed afterwards on our own, but they're all ones that we figured. We can make some actual progress

on. And I'll just stop sharing these lights that we put together for a quick second to jump to the Google Doc, which I've shared. In that the chat for this session, there's a link to it there. It's cuz we talked about last time and questions that were asked with some of the answers, some extra useful, links to three sources that we've compiled. But then at the end is the start of a table where you can sign up to help out with some of the key ideas that I have on the slide

and you can see at all and I mean a few other people have already done this but yeah. Back to this for each of these ideas, we kind of figured we would go through them one by one, but depending on how things are going and serve the time, maybe we would end up wanting to do some breakout sessions and sort of teams of people that want to work on. Each individual one might be able to group up then and make some progress. But it is that we had were trying to make pallets that are

color blindness or Vision. Impairment accessible to be more of the default to have a set of resources and guidelines that could be posted somewhere on the biking. After website, that gives people tips for making their packages more Vision. Impairment friendly, building some sort of accessibility score to let people know if they're their tools are accessible and then Perhaps, this could even be built in to buy a check itself. We talked about, I think this was a total knee afterwards. I can't remember if we discuss this may be a version of butterfly, Fiji repel where I'm colors that are really

similar would be made more distant and sorry I'm just rip out away from each other and I think there are a few different Central ways that could work but also we figured we could go through some ideas of new visualization possibilities of how we can augment plots with non color options and then another idea was to encourage the generation of all texts or sort of like a text that really describes everything that's important and going on in a pot and maybe there are ways. This can be done inside of an automated way

into some of the examples. If anyone has any questions again, I'll just repeat what it's worth having beginning. We set up this session so that everyone comes in on muted but we can all control arm, eat it. Then we can just get yourself if you want to say something or ask a question. So for the goals of making accessible pallets to be the default or putting together a set of five conductor resources, the guidelines. We were thinking that we could basically

with the buy a conductor resources, we could encourage package developers to make pallets. Just be the accessible pallets be the default for their package. But another idea that I think has been discussed is a bit or six colors on the package that I made and I can, I can go through those pictures. I need basically a color panel that is color, blindness friendly. But also, I extended it to be more than just that the eight colors that it had started with, with lighter and darker versions, which is a sort of perfect. But

at least allows grabbing a little bit more about the panel talent to still work with a little bit more complex data. And I don't like it, but I was thinking, one of the sort of action items could be doing that and if they want another person who is maybe made a colour-pop palette that I'm really compatible with ggplot could help me to make it, that would be awesome. And then we we realized it last time we kind of ended up focusing on color blindness just probably

because that's why I told and I both suffer from but there are plenty of other visual impairments. So we wanted to make sure that we open up for other ideas because for example, someone in the chat from the previous session had mentioned that they're not colorblind but they have a permanent double vision. So getting input on how we can make pots better 4 or this type of impairment. That would be great cuz I'm sure what needs to be done is different. Add further to

that has an even greater 6, color palette is likely. Something that is optimal for dance and my kind of color blindness, which is definitely the most common one, but there are less common versions where that might not work. So, we might still need to update that or modify that to me, I guess the most General color palette that can be used as a default and again. yes, having these better balance as an option helps but Having bad as the default really helps where we see anyone who would use your package would end up with a color-blind friendly or

image by default. What is the person who made this comment about the other visual impairment has joined? And if they wanted to contribute or say something more about that, but we can definitely move on, or if you just had any questions or any more input, feel free to unmute yourselves and jump into the description. So for think this was your cited. Kind of bullet point was having a score activity score for a bigger, right? And part of that would also be accessibility score

of the color palette that you use and similarly, the application after that was some sort of a function, which like Gigi repel tries to keep colors, which are similar to each other apart in the figure. So the idea is basically our to generate a color similarity metrics for a better pilot. So, let's see if you have a vector of colors then you get a matrix of bristly. How distinct is each color from every other color in the Rector and the common way to, I guess the most trivial way one could think of is just to look at the RGB distances between two colored, but that is not

perceptually uniform. So they basically a standard call cie lab a representation of every color. In the L stand for lateness is basically an access which goes from red to green. And B is an actress with goes from Blue to Yellow saying these three axes. It represents every color and basically, that is something, which is commonly accepted as perceptual uniform. Color space. So very good job of a schedule. It in the sense, in that space. Good is expected to be

consistent with the perceptual distance between colors in any direction. So that could be used to that, we have resources available for that, and the question would be, yes, you can make a color similarity metrics for normal vision, but if he wanted to make that for color blindness specific kinds of color blindness, we could use color blindness filters, which are already available in. Are in a couple of packages, I think color blindness is one package, I believe color blind or is also another one right now,

as well as I think color space has functions, which Tell you what did you think I would do that? And write a note Pro 10 might see color that you want to pick. Is that right? Yeah, so those one of the color blindness features that I mentioned that I built into ditto seek was a simulated function. It really, the way it works, is it just takes the color panel input, and uses the instructions to can convert them into a version of the colors that simulates, what a color-blind person. Would see that, I think what we could do

when there's there's got to be a matrix built-in in the background but the back end of those functions that that we could use for Yeah. As in the hope is that Busy Bee's color. Blindness, filters are accurate enough or good enough. Someone has raised the alarm on mute yourself and can you meet yourself? Leonardo. Sorry, I was just curious if there's a website where you can maybe a blowed, like a PG or g f mean, like, see how your current plot looks color blind. So I think the color

binder package reports that you can do that, and it basically, it's if it's a PDF. Sorry. If it's a ggplot that you're it, just started to take that as in putting convert it. That is great. If you're in the process of making it around that you recommend, I can just have to get my package. They're definitely screen filters with do that, I think. What do I use? I think I use VI sense or something like that which basically and there are number of filters which we can definitely look them up and update them into the in the document. I think there was one

unshared last time. I'm going to say this fast I think. and, Any of it. So I Wine Down looks like that I'll probably continue with the. So once that says you and that we have a color blindness or other similarity metrics for colors of colors for different color, blindness types of that could be just as an as a whole say how interpretive color palette that is being used in a figure is so it would recommend to use a different palette depending on how many colors you're planning to use other than friendly pallet could tell you,

which of the Say, 4 out of 8 colors that you should pick for a particular figures should be. And the second application would be recalled. I guess the Apple equivalent of a light switches say you have a Disney plot or are you my blood and you want to assign different colors for different clusters of cells and a figure. And a you want to ensure an impregnable, it babe, there's orange green, and maybe some weird form of yellow. I guess it might get really tricky for colorblind, people to identify where one ends and the other starts. So any easier way would be too if

if it all we want to use these colors, I'll be would want to separate them in space and in between have a player which has contrasting with the two similar colors in between. So basically, the function would be similar colors. Are pushed farther, apart and dissimilar colors are pulled together in the final assignment in the figure, So yeah, so busy these other links which I think would be useful where the first one converts colors from the RGB scale to the

lab scale. The second one is It's a place the color difference. If you go to Wikipedia and type color switch for color difference, at tells you I think four or five different methods of calculating. The difference between colors starting from the euclidean distance between the RGB values. And so I think the Delta is one of those has the best defense in the Color Lab space pictures. Bill accepted as the perceptual closer to the perceptual difference between colors and then

these last two are basically functions which would help us map from saying normal vision color space to color blind. It didn't even have any questions on this. Or any comments if you have work. Colors extensively as an illustration if you probably know more about lab space than Dan. And I feel free to chime in Did you find the website that should be able to just how much would it help to just do? So have, like redundant ways to show a different classes for examples of having like colors but then also have a point for myself. I'm not color vision impaired but

I often find it that's helpful especially because sometimes journals with this kind of hard to tell them apart and then they have like maybe still have like black and white. You have to pay extra charges. If any I might not always be possible at this. Good point. I think the next couple of slides, real address. Happy just go. Highest is a member of a sudden, he's a summer fellow in the fatigues lab and he's been working on this for. This was basically data just break from. I think Ruben tries had shared a bunch of

spatial who makes data but I think Suzie an e-mail data where it's just, this is showing you different, I guess tissue types of scatter plot with different tissue types and the only qualifier between the tissue types as the color of these for blotches of cells. Right? And I don't really have any problems with the choice of colors are there quite distinct. And of course, there are only four cell types of tissue types here so there wasn't too much. A problem to find a four colors. And I think this is probably anyway, something that they just shows. So, so what do you want to do? Basically is just

to add a second layer of information where instead of just having colors, you can just argument the figure with texture or patterns in the state. Or let's say, if you have a sparser, got to block. You could say bye and shapes, where you could say, blue, triangles and feta, and red squares and yellow dots or something like that. So, having a second layer of information, which reduces the dependence on color alone helps as, and I think it helps both in case of

Definitely in case of us but you won't let safe once you get into 20 colors even for vision. Normally people, it would help to compare two shades of yellow. Based on what the overlaying texture pattern on those has an example for this particular figure we didn't even as a month, we introduced the bathrooms. We don't even need there to be basically a color as a distinguishing factor. In any one of these colors, I would still be able to drive under five itself belongs to Which tissue type in

the texture. Be readable. And that things like shapes are definitely helpful but I think it will shape the part when you have points that are overlaid on top of each other. So that's a toll showed me this representation and I immediately jumped on it and my initial thought was to private ships first. But for like this it wouldn't really matter because I didn't make sense because the The I guess the orange blobfish are right as in, you wouldn't be able to make out whether what shape of points or what find Shameless actually made

of. So we definitely want to do have some texture and that, but he also wanted the texture should be such that. It perhaps also looks for individual cells so and as well as areas of Vasily denser cells back together, Question her on. One of the things that we started realizing when we started breaking apart, some of the Sriracha matching is this. They use scales to actually reduce to make the customers look better. So the ones that aren't the cluster that are underneath that she made smaller. So, it looks like. So, in this case hair, you may well have other

cells underneath that this may be histology. But if this was a test near Yuma, if you have other cells grow these, and you wouldn't be able to see that happened to Nashua within the cluster very easily, so, how can, and that's one of the main reasons why people use these approaches and all these colors and everything is to try to estimate text Nao, Shih, Tzus around it. So you can see like, you know, whether 90%, Rocky being caught him, but you can see if one particular it is straddles, but if you're using this approach is there

no detangler that you can add into indication the home in like the discussion within within the cluster. Definitely can't imagine having see a fainter version of the same texture covering the entire length of the convicts. All of the cells or an ellipse kind of thing. Very busy, you could still have the annex be there along with a text around that are colored potentially other there. You could say, 45%, This color in Tennessee, more recently built some like hack spinning versions of my scatter and implants and

with those, you can make a plot where you for each of the bins, it'll show what the max label is. And then you can make another one where it actually shows with the same like the street groupings the proportion within each band. That were part of that, Max cover, or Max, pooping thing would be actually been in, right? It would not be a part of things. That would be something on bios here. I'll just I'll go through. Play ideas, I have built into that our seat just really quick.

Trying to think of them that your talk later unless you go through your slides first. Well, it'll be before I bring them up. She has only a scene of a month or so who are your parents? Then do you think the the next to slide my somewhat answer? What Aiden is asking about the city showing to what extent say the underlying cells are? So basically, just I already talked about the colors themselves, I made it to Legend symbols are in March by the falls which is it's weird,

ggplot code but it's pretty simple to do and then color Alternatives, like letter, overlays shapes or fasting are all great. We talked about shapes that last thing you could have a five colors for ten different groups. If you just have five groups in 1 ft 5 in the other, we talked about having ellipses, go around the Grier's butt. Labels directly on top of that means people don't have to necessarily match the colors from the Legends, the group, you just automatically know what that color right there represents.

And then that's really everything that I built in to get a 600 as I'd say, the pint-sized changes and if you have, let's date. Even if you had a large. Wine size in The Legend and much smaller planes phases in the actual figure perceptually and could look different at least it was I don't know if it looks different to people as well but I definitely take something for some other color when it's really tiny. But if presuming are you basically just early Mike for rainy days is where I'm kind of problem showing my age. I got involved in this project and what they did was

they wanted to make the point that the time the people weren't making their days available publicly and it was hindering research. So, what they did was they took one high in pack Journal I think was makes genetics at the time and they took one year. But then basically the start was basically all they are a platform all the way, Publications the year and it was something like around 7 or so. And then it was Pare down for you stationed in Japan around 4:50 and then we divided up into teams and people, basically, each team, got six papers. The job was to

reproduce bigger one and then we were able to go through that last. She provides just how many papers have been published in the journal. In the previous year that actually provided days have provided methods that were doable. And it was basically, with giustozzi paper and it has high impact at the time. Because first of all and and became one that they see, people could size is an instance, fixing the problem, in the field and some time, something like that has more impact than they. Just been a couple of people saying that this is important in the field and saying, like

a light I see this is like some sort of dacious a to what extent that the problem. You don't get the journals behind you actually necessarily making those changes. So is that something that could be done for this like cake? I don't care what channel it is but some something so stupid. If you did, it would actually have an impact and just go through the last six months where they had to kiss me or you might place, which is just do a tech, start to the journals, put it out

and then look at it and say how many colors do I say one of these machines will actually quantify that the issues with that thicker and then you actually have some Daysha to say, you know, of the XXX speakers published in xxy journals in the past year, Basically, these are not accessible in 50% 70% charge because whatever it is a cases and you actually have that day. So which then of course you can use like as a as a pilot a shower for Grants. If you want to actually work in this area, it can be used in. You know, when you watch want to give a talk about it because you

actually have like days are rather than just anecdotal. I find this difficult difficult. I'll see you in a couple of conference computer science day did something but for accessibility in general of paper. So in terms of how screen reader friendly, the papers were out whether their figures help me to text or not, and all of which was basically done for Conference of missions where I can see the lines are probably much shorter. people don't care a lot about this thing, but If you're not ready, if you have, if you want to jump and you can unmute yourself and

or is this from the what is a bit different. So, share my screen. I'm not give you permission, but if you're going to jump to something to talk about, what, yes, I think it would be quite useful to do. And that is definitely something that we should explore probably is not just from color blindness, but also try to cover other impairments. Roman to even just make this very clear Point might be good. I have a particular interest in dyslexia, but that's a complete, the other thing. And like, you know, the financial times is the only like broadsheet that actually done anything about that. No, I

agree. I think if we get started with the color blindness week and then in the discussion of a paper, we are right on that talk about how there are plenty more things that we need to worry about too. But I think if we if we can build accessibility of we could use that to power a review on the accessibility of these. Major knows that, like, this idea that you just brought up and don't need to do every Journal, then you don't need to do a massive time span, but I think you could do something something the systematic.

You know that basically isn't biased. You just took a selection of stickers from one or more Charles over specific time. So that way, it's not by a saying that, you know, the dates of our generation are the days of our generation, has something else or whatever it is. But I think once you have something that's systematic. However, it however it's done is facing not biased and unbiased. I think that gives you Daisha that gives you play. Marie days are for whatever you want to act like for the grounds for the, for the for the reason of

developing this for the talk, for everything else that you need to know. That's a good idea. I'm just wondering how to design a questionnaire for that. Again, if it's going to be a Crowdsource cousin sp118 people on the call and maybe other people have much better ideas. If I were, you know, I would just say, get yourself and done and then, you know, a couple of people that are color, blind, people that are color blind and just say how many customers do you say in the speaker? Can you see the cluster

groupings? What does this look like to you? And then maybe do some sort of a computer-generated picture what it looks like but you know, you don't need to do that for every single one, you just need to have I think they said just to support that this is a problem as a human subject. I don't know. I think it's the subjects are all hers on the paper then. Do the truck. You know, if it's just a case, like if you want to do something, really systematic can comprehend. So then you might need to do a crowdsourcing but

I'd be tempted to just say, right? We just take one year. In three, journals in the full text and bring them down and just look at them you know and then just see how you're going to have it. Maybe case that you know you have to actually look at 50 figures It's probably doable but yourselves cuz you're the experts I guess. Probably, I don't know if there are some capture Services, which could be very good for those and that okay, how many clusters in this? How many different colors do you see? As the cops are a dozen Red, Butte Garden Center.

How many diciendo? How? Reading, all of these journals online. Parents of printing it out, if I have a bigger screen, it would really help when resuming. But if let's say the the figure itself is not a vector image or if it's not high resolution than it might be harder to do me, just because I legally permit. Shapes. You can click, let's see what's happening because of the main. Bright if you're actively. So I mean, there's a simple plot. I have more complex thoughts here from another for sample, maybe some of these colors on there. On the

left side here, I'm going to just run it. Has a lot of points but like, you can change here, have an option on the shiny app color scheme, and actually, the friendly Nation, but basically just a lot of options for different color scales. I actually built that into did I see kids while I just didn't connect that with color blindness, but you can convert almost any ggplot object to a popplio objects. Gigi Papa and static versions which will have all the information. So

I just seen that you make that the focus of one of your suggestions I think standardizing that as a Means of saved. Communication channels to your paper. So just like you say that today dies, a table at display the cortisone available place. And then what are you going to tell a companies like going to help you and like one of them and so that's kind of what I'm awesome. It's like you're trying to be smarter than the people right here, trying to bring them in.

no, that's that's a great idea and I think that's definitely something that would I guess become more as an interactive Graphics would become more commonplace. In the near future, I buy the atom as part of the publication itself. I can see that as opposed to just being a standalone web page where we are. Example publishing. We're like at 1000 was one of the first one, I think that's a great suggestion and I really like the idea of trying to do some sort of like, even if it's just like a two-page letter, but some sort of review of

how good the accessibility of the bunch of recent papers are not. Could be a great suggestion to add up my leg. Play. Just like the other batch effects. And then they actually presented different and cases where this was at the time. Was that many cases? I think you kind of need to have the data and so he has more strength if you have something to back it up, And I wasn't the idea. I kind of had is basically look at these highly cited papers and take their figures and show them

how it can be made more accessible, and I'm just their fingers. What could be done to those people to make it more Equitable and use battery colors? Use wprs happening in the Put on the puppy page. We had one other example of a alternative method for something that's often represented his collar. So I just figured, we might as well. That's right. Oh yeah, this was basically dumb luck by Melanie locked in the body lab. So I hear about me kind of what you wanted to do. Is we wanted to see how they the a

gene expression of 32 jeans. Are there any latest features between two cell types of tissue types as changing across? This is from of the GM data, sets the speaker, so I just picked to rant and arbitrary jeans. So TT. Mmt one is shown on the Redskins tomorrow. Pick the red has the higher DJ expressionism. The pr quesadillas on the blue scale where I can see the morrow pig that has the higher the intensity of the expression of the issue. As a strawberry, we were trying

something like this, but then the issue became very well. Let's see. Both of these genes are expressed be going to the purple scale which becomes really tricky to figure out to them as if you're any more blue or more rather than trying to exercise has opposed to just seeing what it is. What could we try to do? Is basically, we just let each of these circles on each circle. He represents a slide and each. I was split into two halves of a circle semi-circles where

the lower half is, showing the blue scale and the upper half is showing the Redskin. So I have them for me. It's really clear how that the pr cable Changing dynamically over the space and the other one is as well and apparently it's also more interpretable for people that normal vision. So this is just an example of the little things that we could do and figures to try and keep the colors apart as possible, and not Bank on say color mixing to provide any meaningful information.

I think if it's, if the bins were a bit bigger, be resumed in a little bit more, if he comes with you. Visualization is a more difficult time. So I think there are problems which are common. Which are not just about color blindness in Disney and you might be talking about overlaps and all of these things, right? Special. Probably, you don't have those problems. Everything is separated by itself. So I think the the disadvantages are largely colorblindness based in special Adam and if let's say you have a 20 different cell types based on what kind of

immune cells or cancer cells, they are, then you might run into the same problems as you might in Disney. The part that last example where you're literally just looking at two cells white and gray prettier I guess again. I actually still like how. I got data visualization class. If I learn some things in my classes, started things that night if you can introduce them in a Keurig to them then yeah. That's a way to just sort of, make sure that those things are right now in

Green Drive in my student finance. I try to remember the color blind if you can because I don't have a setting. I did very and you didn't try to make it color blind friendly and it's just, I mean I've been trying to get better about that, you know, when I when I prepare Plus for Publications but it's not something that you not really the first thing that I think about it. And it's also not like something that I would sort of know, I taught formally. So I think it's one of those things where

you kind of like developing I put it. I have not either. Even if you had things are changing really fast. Like one of the things I've been to like smoothies bigger. Thesis to the visualization in different stages and stuff and things that they might have talked about a few years ago are now difference. And even if you look at it, like we said people that are doing data visualization for things like upbc Financial Times, you know, your New York Times and things like that. So she got a couple of those people and

state departments. Give talks. Things are changing and they've changed the locks on the stickers that you know, people presented a couple of years ago are not the visualizations that are being presented now and I think if you look at any visualizations is that Justin likes New York Times the normally have now like a web front end to go along with it. So a lot of that is don't you are so I think things are changing a lady with important as the default sargood default and and that people need to be aware that their packages should have

reasonable defaults. So you need something that basically where it raises the weariness and then provide those basic tools. Such that like the default is always relatively reasonable. I was wondering if that's part of say bioconductor conferences itself and there should be I guess we're going to try to have a session about as in someone would explain from a usability perspective or user experience perspective as to how to design your defaults or how to design your because I'm both you and Dan and I are The times

of consumers in a sense, right? And we are trying to learn it on the way, but I would assume they're people who are a special and I think the feel of G is there. A lot of the information goes out to the general public. They have thought a lot about accessibility and interpretability of their figures. With the way the conference is organized, its you volunteer. So, volunteer last year, it was just a called anybody who wants to help, you know, it's whoever signs up to help get to. If this isn't a top-down, this is literally like join

if this is, you know if this is important. Then you know, the best person to drive it as you conference. You think that would be good speakers and I just put it out there and just go for it? Definitely. I mean I've been in communication with the the cab and I hope I've been thinking about that already so I might just do that if I can but I think we're towards the end of the time. So I just wanted to I wanted to just come back to this. Google doc again and just in Courage where to buy some go. So I can share encourage people if there was a

particular. You had been. Out west and I can even be helping out with the paper at the house. So just sign up here. It can you post on the slack Channel or varies from the link? Yea, I can post in the fact you the link is currently in the chat for this session. Then just an idea to talk about. I would definitely make a Splat channel for this as well, so people can join and contribute or do what you need to make a slap channel for this. Anybody can make a slack

Channel and and then, you know, organized around that way to go forward in this. yeah, I think I'll make a channel called accessible for his cuz it's already cold as and that would be Yeah, we don't, we maybe we don't need that, I'm just if you want to you can just give your name and then especially if you're already in the slack that's totally fine. Thank you for driving this. This discussion we had, so that's actually really cool things. And thanks everyone for joining and I'm excited for what we're going to do next.

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