the new Netflix series brother son has officially been cancelled and will not be coming back for season two and a bunch of people are talking about it yeah a bunch of people sent me this and i'm not gonna lie this might be one of like the quickest cancellations i've ever seen because we just got done talking about it launching anyway guys make sure you like subscribe turn on your notifications this has been sort of like circulating news in the asian americans that are interested in entertainment community this week right yeah no i mean i think a lot of people are reposting about it because everybody was waiting to see if brother son was gonna get a season two obviously this is a show that i watched a lot of other people watch but obviously not everybody watched because if everybody watched it they'd they'd bring it back hey shout out to sam lee friend of ours him and justin chin and her they just got done doing their talk show rounds like two weeks ago yeah but i mean that's how it is right the show comes out and they get they get the views maybe i think Netflix had some very strict metrics and numbers that the show probably needed to hit right within the first couple months and it didn't hit it right i guess it was like uh it fell very short of it that is according to the article right i will say this and nowadays in the streaming analytics error decisions are coming quicker than they ever did right oh no they're like oh two weeks in didn't hit the numbers done do you think though that there are extra this is the conspiracy part and we have to entertain it because we know that there can be some legitimacy to this were they extra quick to cancel it because it was asian they could they have just held off the decision because then it looked like they just couldn't wait to chop it down no i don't think obviously netflix has anything against asian people no i mean netflix has a ton of great and successful but you know what i'm referring to and this initial boom of like let's approve everything asian but then cut the ones that don't you know perform quickly if this sort of like process might be in session well man you know it's just like any other business it's about the bottom line it's about money because at the end of the day listen the show costs money to make and if they don't think it's worth it to make another season or they don't have the other season written or they don't know where to take it because do they take it to taiwan because at the knowing at the of this the ending of season one taiwan seems like the next logical place to take the story but they can't film in taiwan so i guess they kind of left it you know like maybe they just don't know where to go with it hey listen guys the comments were very split some asians were happy to see it get canceled which is interesting we're gonna get into that some people were in the middle some people were sad and real quick i need you to give your hot take did you like the show as somebody who watched the show i liked parts of it and i think part of it was very strong and part of it to be honest was very cringy now shout out to all our friends who were in it sam lee jenny yang june lee yoshi sudaso they got their shot i thought they all did their thing but yeah execution wise nah there was definitely some parts where i was like and then there were some parts where i was like oh i like it there was parts of it that felt like a christian movie director that had never seen an asian gangster film from asia like god put in charge of this gangster scene and i was like well this is so weird yeah so so the of the friends that hated it i have friends who hated it they compared it to everything else oscar winning movies they were going to compare it to a lot of the korean films that are coming on korean shows they which were maybe overall better they said the show was unrealistic it was corny it was your girlfriend didn't like the show no my girlfriend did not like she hated the show she hated the show um i think a lot of like asians from the street world maybe they thought it was kind of unrealistic and goofy well because it made the azn street world to be honest looked like a joke yeah but i think the friends who loved it they didn't overthink it they didn't over examine it they were just like oh it's a fun show with a lot of badass action i like michelle yo so it was cool right right right and i'll tell you this michelle yo is going to be okay she got cancelled from abc on disney plus now this show got cancelled and she's still going to be in 63 things next year anyway let's just get into the comments section somebody said but they keep renewing emily in paris and river dales and stuff what the f but here's the thing is literally guys if you guys know how netflix operates there are very analytic like tech based company they literally just go off roi stats yeah i think that um on the asian internet asian american internet a lot of people are talking about this but you have to understand how many people in the world have no idea that this show even came out right somebody said listen guys i felt like whenever all the critic reviews came out it was just rose colored glasses everybody felt the need to support a pro asian male masculine show that was like kind of gangster kind of illegal and kind of cool but everybody was just not being honest with themselves because not all representation is good representation guys there still has to be a minimal line of execution ability wow yeah i think there's some truth to that comment um somebody just said man i couldn't even make make it through the first 20 minutes of course andrew this turned into a bunch of people pointing out everything that they didn't like about the show gangster scenes unrealistic this part seems serious this part seemed absolutely off the wall wacky plot holes galore people really hated it when the what the dancing tai chi grandmas like she stopped the gangsters oh man that's probably that was a cringe show that was a cringe all my friends in the show i hope you guys get more work after this it might have been the worst asian gangster scene i ever seen in my life yeah by the way guys the actors our friends who were in it it wasn't their fault how the show turned out they're just playing the role right right right um other people were saying oh netflix is losing uh money and they're just blaming it on the asian shows blaming on their dei shows somebody said man listen guys with warrior getting canceled abc getting canceled all these asian shows getting canceled it goes to show you what happens when asians don't have an asian american network for all these shows to live on because you know how uh obviously there are more latino networks they tend to be more spanish based but there's certainly a lot of uh black entertainment networks and then or verticals at least whether it's digital or in analog but then like asians are always existing on mainstream platforms because there is no asian centric platform i guess i mean you would agree that that's that's true i don't think this asian network is going to even have the money to produce a show like this right because you're saying where would the capital this was like millions of dot like i don't know how much like what like did this show not cost more a million dollars plus per episode for sure yeah probably yeah that's why they're so ruthless with their ROI yeah calculations that's why netflix is like cool we made the show great it didn't make the cut we're done that's it um i hope this doesn't spell the end for like triad shows i love triad shows but i will say this it's very difficult because like the azn world in terms of the street world i definitely think it's perceived or whatever more southeast asian so you can't really bring it to this like taiwan gangster and then taiwan over achievers that are like nerds that are like in orchestra getting straight that there's just that to that to how it manifests in america there's no connection between those triangulation of those three worlds yeah if i had to put it plainly i think the show felt too goofy to be an actual gangster flick and it was too dark and gangster to be like a full-on kind of jackie chan comedy you mean like fresh off the boat fresh off the boat was clearly in the silly billy's wholesome yes that's why fresh off the boat worked even though some scenes of fresh off the boat were cringe it was like you know what it was supposed to be man it's supposed to be a family funny show about kids the color grading was all bright and sunny so my thing is if there were to be a season two in my mind of brother son i would like to see it go darker even darker more gangster and have it take place in taiwan now maybe i think just any other taiwanese gangster flick which i've seen some takada yeah dakada or there's like multiple taiwanese gangster films the gao shou hei shou hui they're way darker and way more serious oh man they're they're dark and they're way cooler to be honest like those are just cohesive pieces so anyways guys we're not here to rag on the show because honestly i enjoyed a lot of part of it's a lot of part parts of it but i'm not also going to be shocked that you know our agents get to get another chance to do something conventionally cool or is it back to sunny yes yes i think so even though these were all shows that were approved maybe three four years ago and then got made a couple years ago and then are finally out i still think asians are getting more shots but there was definitely a surge of asian content and not all of it did well do you think they're replacing it they're like uh you know shogun that takes place in japan plus we got the uh white protagonist uh yep shogun in brother son out david does it kind of go to show you that when you film something using a lot of asian americans it's tough on where to put it is it you mean the cultural space is it a goofy fun just comedy or is it are you trying to make asian america seem very dark crazy and dangerous and gangster is it the corruptor or is it a more of a jackie chan but not jackie chan the foreigner you know i felt like there was a mix i thought rumble in the bronx had an amazing mix i thought older jackie stuff before he got super goofy like the suit that was really uh the best triangulation in my opinion but you need the personnel and the writers and everything to pull it off i like rush hour series rumble in the bronx let us know what you think in the comment section below until next time we the hot pot boys be out peace


yo what's up dudes so today what we're gonna be doing is going over my vocal chain so let's check it out so when when every time I start a session I will go to my templates I've created a template for this okay so when I click vocal template it's all gonna pop up right so let's do that first and then I will show you some vocals running through it so vocal template and and what this is gonna do is it's gonna give me my main vocal right here with all of the plugins that need to be on there and then it's already gonna have all of my buses on there so I got the vocal bus routing to this the reverb bus routing to this another reverb a delay bus a wide meaning a course and then parallel compression okay so in my main vocal these are the plugins that I use I have NLS channel stereo okay don't ask me what it does it basically just gives you like a little bit of saturation okay and it's like when when I link this right here to this NLS bus over here it gives the vocal more saturation all right so that's the always the first plug-in on the main vocal and on the bus vocal the vocal bus all right my second plug-in is my tune all right I always keep my tune on the preset of light tuning and then I change the key depending on what be all right so if I'm cooking up a beat in G minor then I'll change my key to G minor all right these two plugins are not turned on so don't pay attention to those the next plug-in I do is an EQ and as you can see this is subtractive EQ okay I wrote out these low frequencies I wrote out these low frequencies over here okay I pulled out some of these frequencies right here in the 340 some of these problem frequencies I pulled out a little bit more in the in the 500s okay and and then over here I pulled out some in the 30 30 30 33 3400s okay next we got a DSer this right here is also corrective EQ the frequency that I'm attacking is 42 37 that's where you get a lot of the a lot of the S frequencies so I throw a DSer on here and I attack some of them frequencies the next the next plug-in that I throw on here is a EQ to to boost some of the good frequencies that I like okay I I do remove a little bit more of the low frequencies you can see right here I'm removing nine decibels at this like three three fifty area low mid frequencies I'm removing three decibels at this point eight nine area I'm removing a little bit more of these problem frequencies with the DSes and then you can see I boost right here I boost a four point five decibels right here in this a thousand area and then the next we got the CL 76 compressor the bluey revision you guys can see my settings hmm we have a fast attack and a slow release then I have a R box some more compression and then we have the R compressor some even more compression all right so let me load up a track so you can see what it sounds like running through that compressor okay let's check out padded room what I'll do is I will play the vocal track just one solo vocal track I will play that without the busses and then we'll start to bring in each one of the bus tracks so you can hear what they do okay so as you can see there's a bunch of different vocal tracks right these are all my different layers but after I set the tune and record on this track I'll just duplicate it and then I use the same settings for every track for my rough mix of course like as you get into your actual mix you are going to have to tweak tracks depending on background vocals and things like that but as far as like a rough demo mix it's really all I do okay so here is the vocal I'm gonna turn it up a little bit because I have my vocals dubbed so it's like when you double your vocal you got to turn the volume down on each one okay so but I'm just gonna play a solo vocal for you guys so you can get an idea of how it sounds okay so this is with no bus on there let me turn off all the effects and as I bring each bus track on there I will tell you guys what effect is on there okay so here's the vocal by self so that is the one vocal with just my vocal chain no bus channels so the first bus I'm going to introduce is the vocal bus and the effects on there are the NL bus that gives it saturation we got some more compression we got the Saturn plug-in that gives it some saturation we got the Q10 boost in some of these really high frequencies we got some more de-esser and then we got some more compression okay so like this compression on the end right here is optional all right so this is before the vocal bus who really cannot run so well really cannot feel this is after life feel like a padded room swim feeling so insane haircuts non-detained lost it all every dead thing I was so you can just instantly hear how much more presence you get by running it through the vocal bus running the signal through the vocal bus and giving it some some saturation some more compression some more EQ so the next one I'm going to show you is the reverb okay so on my reverb I just throw like a fab filter vocal gloss on there and after my reverb I EQ all right I cut some of these low frequencies and I cut some of the high so it's only giving me the reverb on the frequencies that I want okay so this is without and then I'll introduce it so my first reverb is a short reverb the second reverb is a long reverb okay so I will introduce both of them as a place who really cannot run to well really cannot feel safe whole life feel like a padded room swim feeling so insane haircuts non-detained lost it all every dead thing it's very subtle but as you can adjust you can adjust how much of the track you want to send to the bus channel so right now I'm sending negative 10 decibels to reverb one and I'm sending negative 12 decibels to reverb two so that determines how much I want to send but then I can even raise the volume on the reverb effect over here and it gives me even more control so listen who really cannot run to well really cannot feel safe whole life feel like a padded room swim feeling so insane haircuts non-detained lost it all every dead thing I was up in my pocket sweat like I'm running around in the damn rain okay so the next effect that I have is a H delay a 1 30 second and this is what it sounds like who really cannot run to well really cannot feel safe whole life feel like a padded room swim feeling so insane haircuts non-detained lost it all every dead the next is a delay to this is a little bit of a longer delay this is a one bar delay who really cannot run to well really cannot feel safe whole life feel like a padded room swim feeling so insane haircuts non-detained lost it all every dead thing I was up in my pocket sweat like I'm running around in the damn red who really cannot run to well really cannot feel safe whole life feel like a padded room swim feeling so insane hair all right so I'm not gonna show you that one right now normally when I do that I will automate it so delay three this is automated so I'm not gonna show you that right now because that's for a whole other video so the next one I'll show you is the course effect who really cannot run to well really cannot feel safe whole life feel like a padded room swim feeling so insane haircuts non-detained lost it all every and then the last bus is parallel compression so this is our box and a little bit of driver so a little bit of distortion so listen to without it and then I'll start to introduce it all right who really cannot run to well really cannot feel safe whole life feel like a padded room swim feeling so insane haircuts non-detained lost it all every dead thing I was up in my pocket sweat like I'm running around in the damn rain how I go from feeling so high to feeling so low in such a short time late nights I was on the ground and then when you combine all the effects all the bus tracks is like you just get a much stronger vocal so let's listen to with the music who really cannot run to well really cannot feel safe whole life feel like a padded room swim feeling so insane haircuts non-detained lost it all every dead thing I was up in my pocket sweat like I'm running around in the damn rain how I go from feeling so high to feeling so low in such a short time late nights I was on the grind this husband shit is just a waste so I muted my dub so this is just one single track okay who really cannot run to well really cannot feel safe whole life feel like a padded room swim feeling so insane haircuts y'all hear that little delay when when I just unmuted delay three I have it automated to where it only comes in in the spots where I stop rapping so check it out who really cannot run to well really cannot feel safe whole life feel like a padded room swim feeling so insane haircuts non-detained lost it all every dead thing I was up in my pocket sweat like I'm running around in rain I will show you guys how I automate those delays in the next video thank y'all so much for rocking hit the like button share subscribe whatever


I'm saying God yeah, I am again.   I'm introducing you a co-j and ambi make some noise On my left side taking the harder challenge of being the one we have some jizzies And I said shout to the team on my right for taking it because a lot of people are always like really like has this thing about taking two I'm on vows. They want to be the two that would be the one whatever everyone's got two big egos But it was separate sides.   Why aren't they growing?  I'm Oscar P.   I swear You trying to box well, I got the mind that'll try and block see this fire will stop Michael like Myers doc I swear You know the reference Nothing but jokes battles So I wanted a serious one You guys can understand right so I took it upon myself to go against Coljane some fact that No games This is no games Because it's serious. There's no games. It looks like I'm battling to you guys and co-jet After taking a terrible loss to HK I've taken a hook terrible loss to HK. I needed redemption.   No, this is where Jixi's real rhyming starts. I'm like ministry Checkpoint, I put more work behind the bars except Except for that one I beg you don't act tough during this battle I will could you get a repeat of the retrieving in the beefy retreat and be you're just online to a beefy retweets I'm like leave them talking because that's all fake computer talking no walking like Stephen Hawkins If I was to punch you cojay would run away Come back when the fire can cease that means he's only present after the action like ing if you get the reference So what you thought I couldn't handle these two blokes It's a battle couple punches a few jokes, you know, what's coming next stop acting You know, I'm kind of thirsty Rosie. What'd you get me?  I think You And he always talk about the cans that he's great, but I know Essex the land of the vanity slaves He ain't the man that he claimed you hide him behind that image.  You think so just nice You think so just nice and gift of the gab nor see you choking twice So no smack after that crash like the hole from flight. See I go overboard with it like I'm rolling dice No reaction. Yeah, no reaction. I expected that shots always get aired when a soldier dies. I swear Stop acting as a soldier Or we'll see salt for later. I'll box this fruit like he was ocean spray the best thing The best thing about you is woozy The best thing about you is woozy.  That's lowest lane Now you in deep waters with twice the beast like the boat. No, we're made see and be supportable Like the rogue Jonah played we coldest rain. You'll see in a second So behave wills. Bitch are getting trouble with calm like focus man.    No, this is me breaking rules Will's he get involved?  Will's he get involved?  There's all killers in this circle. I'm in different hoods Getting heavy bars from small packages. My coke's like kid verbal I would shot to your mums That good that we're getting me. I shot coke to anybody. I'm like a vending machine When I say vending machine and he got happy Reminding him of his favorite place to snack He's been doing this change on Craver Pack is if he didn't fully shake and bang it till he dropped he laid drink his pot while he ate His favorite sandwich that's snack bars Ambi likes snack bars, rebels and Maltesers You guys don't like it pretend Kojay did it On Twitter you can find Ambi doing anecdotes about his girlfriend and Kojay saying hi to the haters.  I did you know I'm not saying she's fat, but she probably walks through the door like this You just told us you sold coke That's hardly bright watch your cargo and sure it's hard to find because if you rode by my roadside Did it be like known five when you catch a hollow selling charlie lines, but So you're best find your hurts because you trying to survive the verses as likely as a timely reply from earth See my mind superb every line is divine in words like I ran with the Mayans word.  They were trying to make I get it They're way more Michael Kane than Isaac Hayes and they didn't even do it in a stylish way.   I've got a good shot. So that's why I've always got extra clip like a Frankie Fraser bow But I could see I could already see the hate on the comments on youtube Everyone sleeping on ambi because there's room to I Can't see I can already see the hate on the comments on youtube Everyone sleeping on ambi You standing still You're sweating bad I should just me and koji should just have a one on one Because we're 2012 Your your rap sheet ain't long enough.   I guess his mind isn't all there It was like the dream works kid because that line only caught air, but


Unfortunately, in scientific publishing, we're typically limited to about five figures per paper. And while we can have multiple panels per figure, the more panels we get, the smaller each individual panel gets, making the text and the points harder and harder to see. So if we have complicated microbial ecology data, like I've been describing in recent episodes, as we have more and more panels in those figures, it just gets way too hard to see. And your figure ends up being basically the size of a full page, which is not ideal. So what do we do about this? Well, some people have taken to merging effectively different panels together to have one figure or a small number of figures that represent the amount of data that you typically find in many figures. Is this a good idea? Let's see one approach today and I'll let you know by the end of the episode what I really think of this approach. Hey, folks, I'm Pat Schloss and this is Code Club. In recent episodes of Code Club, I've been trying to rehabilitate a figure that my lab published as a supplemental figure in a paper a few years back, looking at the variation and gut microbiota of people with and without Cluster Deoides difficile infections. Along the way, we've been also developing a rubric that I have at least kind of handwritten down or in the back of my head of how we might think about interpreting and assessing the quality of different visuals that we see in the literature, as well as visuals that we make ourselves for describing what's going on. One of the things we've talked about are pre-attentive attributes. Pre-attentive attributes are, again, the things that your eyes first see when they come upon a paper. The two strongest pre-attentive attributes are the position on the x-axis as well as on the y-axis. In an ordination, we use the ordination technique like PCOA or NMDS to separate the points based on their dissimilarity to each other on that x and y-axis. In PCOA, the x-axis represents the axis that explains the most amount of variation in the data and the y-axis, the second most. We've also used a secondary pre-attentive attribute, which is color and grouping. The coloring is the coloring of the point by the treatment or the treatment group or the diagnosis group or the disease group that the samples correspond to. In our case, we're looking at healthy people without diarrhea, people with diarrhea and the people with diarrhea as well as a seed of a seal infection. We used color and the coloring also allows us to group the data because if I see a group of red points together or blue points or gray points, my eye kind of integrates and pulls those together. We've also helped this by putting ellipses around those three different groups. And so that secondary pre-attentive attribute really helps our audience to see the groupings that we think are most important. Great. In our ordination, we already have separation on the x-axis and y-axis. We have coloring as a pre-attentive attribute. As well as those ellipses to group by disease status. And so looking at figure 1a, I wonder, can we also add another set of information, which is the diversity of those individual samples? Could we maybe change the size of the points? This is called a bubble plot. So by changing the size of the points, can we map on diversity information? And so I would consider this kind of a tertiary level of information. It's not my primary emphasis in looking at the plot. My primary emphasis in looking at the plot. Again, is on those x and y-axis, the separation of the points by using color. I'm separating perhaps by disease group. And so then this third level or fourth level, maybe even of analysis, would be looking at diversity by mapping on information from what we already had in figure 1a onto those ordination. Well, that sounds like a great project for today's episode of Code Club. So we'll see how we can do this in R and R studio. And then we'll reflect on whether or not this was a good idea after all. So if you're just joining us for the first time, welcome up along here somewhere, I'll put a link for a video on installing R, R studio, the tidyverse and getting the data that you need to follow along if you're interested. Also, if you want the code that I'm starting with, go down below in the show notes, there's a link to a blog post that has the code that I'm starting with here today. So this is where we left off after the last episode of you'll recall incorporating the percent variation explained on the two axes. I think this looks pretty nice. I'm still a bigger fan of the NMDS, but working with the PCOA will help us to kind of move forward with the progression of these episodes and where we go next. Anyway, again, what the goal is, is that I want to size each of these points according to the inverse Simpson diversity for each of the points and we'll then get a different sized points again, depending on the diversity. So how do we do this? Great. Well, I've already gone ahead and in this code that I've given you, I've put code for reading in the Alpha diversity information and reading it and joining it to the metadata and PCOA information. So we now have one large data frame, a metadata PCOA Alpha that has all of the columns from our ordination, our metadata and our Alpha diversity information. We now have our GG plot and I want to add size as a variable and I will go ahead and put this on a further line for our mapping. I'll do size equals in Simpson. And that should be pretty good. That should do what we want. So let's go ahead and give this a run and see what we get. And so again, this is a bubble plot where the individual points are sized by the value of the inverse Simpson index. One of the things we did was earlier, we turned off in GM point. We did show legend equals false. I got some feedback on Twitter and elsewhere that people hadn't known about this. And so I'm happy to show you that. Well, now we're going to turn that off and actually show the legend. But don't worry, we'll come back and we'll see another way that we can turn off the legend. So if we run this, we now see that we have two legends. So we have the color corresponding to the disease status as well as the inverse Simpson. And so we see that this circle size is inverse Simpson of 10 and this larger one is of 30. Now the thing to know about human perception is that our eyes interpret area, not radius. And so that makes it a bit challenging. One of the things I also notice is that I've got some circles say down here that are actually smaller than 10 and don't really fit in well with this range of inverse Simpson values. So what I'd like to do is maybe clean this up a little bit. Another challenge that I see is that these normals are healthy individuals are gray and they're large. And because they co locate in the ordination, they really all fall on top of each other and just like this big gray blob. And so maybe that 30 is a little bit larger than what we really would like to see. How do we turn this off for the color and keep inverse Simpson? Well, we can add a new function called guides. So in Gigi plot, those aren't really called legends. They're called guides or scales. But what we could do is we can say color equals none. And we can also say fill equals none. And that will get rid of the legend for both our color as well as the fill that we use for stat ellipse. And then we will also add in size equals legend. So you'll see that gets rid of the legend for the color and the disease status and leaves us with a legend for the size related to inverse Simpson. Again, we want to clean this up a little bit and make it better. So to modify that legend, we're going to use scale size and scale size allows you to modify the radius as well as the area of your plotting symbol. But know again that human perception, we tend to scale by area and not by radius. And because the size can get quite large, as we saw, what I'll do is set range to a vector of small to large values. And I will do, let's do say point five to four. And let's give this a run. Setting that range now gives us kind of smaller points than what we were getting before, where they could be up to six. So they'd be even, you know, twice the size as what we're seeing here for the largest points. One of the things I don't like about the legend is that it doesn't really have a bottom end, right? So if you had like zero, there's not going to be a point there because it's like zero, right? And so, you know, this point down here where my crosshairs are doesn't show up on the legend. We don't have a good sense of what that diversity value is. So we want to modify scale size very much the same way that you can see right below it for scale color manual. We'll go ahead and do breaks. And I will do one, 10, 20, 30. I'll do labels will be the same vector. And I will also do limits of C zero to NA that NA will let the upper end kind of float freely. I can also do name equals inverse. Let's see if it'll take a backslash inverse Simpson index. I think that's going to probably look a little funky, but we'll see. And we'll go ahead and put these each on its own line. So it's a little bit easier to read. Let's give this a run and see what it looks like. Yeah, it does look a little funky. Maybe we want to change the size of the font there. And that looks pretty good. We could move the legend down a little bit so it's closer to what's going on. We've seen this in previous episodes. Again, down here, legend position. We can set the X and Y coordinates relative to its position in the plotting window. And I think it's the center of the legend is basically where it's getting plotted. So we want it to come over to the left a little bit. So let's do 0.8 and down a little bit. So let's do 0.8. So that's maybe a little bit too close. Let's move it to the right just a smidge. So let's do 0.9. Again, it helps to do this in the actual format of the figure that you're going to be working with. If I was doing this down in my plotting window within our studio, it would look totally different. And I think for reproducibility's sake, we want to be able to script all of this as much as possible. That looks decent. The title of this legend seems a bit big. And so I think what we can do is legend title. We'll do element text and we can then do size equals. Let's do 12. I'm not quite sure what that will look like, but we'll give a rip and see what we get. So that made it, I think, bigger. Let's go ahead down to 8. Again, this takes some tweaking. And as I mentioned, it's best to do this within the format of the image that you're working with. I think we've got a margin problem that the box is going over the inverse Simpson index. And out of two minds, we could either remove that or we could go ahead and. Yeah, so we could either remove it or we can fix it. And so we're using a negative margin on the top. So let's go to minus one and see what that looks like. Yeah, so let's go ahead and do zero. That looks better. You know, we could even maybe go to one. I think that looks pretty decent. And so again, now we have the size of our plotting symbol and in the legend corresponding to the full range of points that we see over in the ordination. So let's look at this figure. Now that we've got it looking perhaps about as good as we could hope to get it. What do we think about this? What do we think about mapping that tertiary variable of diversity onto the size of the plotting symbol? Well, you know, I think I think it's clear that these points down here are one because they're so small or they're really close to one. These other points, I think, you know, these are difficult to resolve probably because we have so many points here and they're actually large points. So they're points with large diversities, but it's really difficult at this point to differentiate between the points. We could make their alpha smaller, but I don't really know what it means to have like a blue and red point overlap with each other. It just kind of gets a bit muddled and isn't really ideal. Again, humans are really bad at interpreting differences in area and, you know, while I can differentiate between one and 10, I think 20 to 30 for me at least is hard. And if something was 25, I don't know that I could tell the difference between that being 20 or 30. And that might be the difference that we're expected to see between the different treatment groups that we have. And so it really doesn't help us. I don't think if we look at figure one, a we're the average or the median, I forget what we did for the non-diarrheal control. So the healthies was about 10 and for the diarrheal controls was about six. And so that's, you know, we're kind of looking at points between that range. And it's just difficult to see what's important, right? And so, yeah, we can size them by diversity, but I can't help my viewers see what I want them to see in this, right? If I were to say that people with diarrhea and people with diarrhea and C. diff have lower diversity than healthy individuals, you know, I'm not convinced that they could see that with these data because I mean, it's just there's this mess over here and there's kind of points over here that are similar in size. And I don't know, you know, I've got some smaller healthies points in here kind of suggesting, you know, diversity may be down around five or six. And so I don't know that that helps. I don't know what helps to merge the diversity data on top of the ordination data. So what else could we have done? Well, another approach would have been to take the disease status and instead of mapping that to color, we could have mapped it to the shape of the symbol. And then we could use color to create a color gradient corresponding to the diversity index. And well, that certainly has some, I don't know, attractiveness. The problem with that is that if I had like circles, squares and triangles, my eye is not going to be able to integrate by shape as well as it can by color. Right. Like I can really help the viewer to see that there's a lot of red points here, a lot of gray points here, even if I don't have the ellipses, right? That because all those gray points are together, they're together, right? And so that's the color is helpful in this case in a way that I don't think the shape would be because we have so much data and it's it's highly variable. Right. The other problem with color on a gradient is that say we went from like white to red or white to blue. It gets really difficult to differentiate between say like 70 percent blue and 100 percent blue that we just don't have that quantitative of a grasp of variation in color. I know people love it for heat maps, but that's really one of the problems with heat maps is that people can't visually interpolate colors. So I really feel like this is a case where we should let the ordination do its own thing looking at variation in community structure. And we should have been a separate figure for diversity information. And so this comes back to something I constantly preach to people, which is that we should strive for our figures to do one thing well. And so adding this is now making it do kind of one thing poorly. Right. Like sure, it does separation by space well still. But it then adds on all these different sized shapes and it doesn't do that well. It doesn't help us to see the variation in diversity very well. And so we should save that for a different plot. And what I always tell people is that if you're contemplating making a figure, draw the figure to answer the question you want it to answer. And so if you give me a figure and you say, well, I don't really have a question that I'm just kind of showing data. Well, that's a that's a loser. That's not going to work. But if you say I want the figure to show this and this and this and this, well, stop, you're trying to show too many things. So really try to simplify the message of your figure down to one thing, maybe two things if you have to. But make sure that if it's doing two things, that it's actually doing those two things. And I think what we see here is that it's really not doing a good job of differentiating biodiversity in the next episode. We'll start looking at how we can differentiate biodiversity. We'll start pivoting from looking at this ordination to going back and looking at figure one from this paper. Anyway, I hope you found this discussion useful of creating a gradient of sizes of your points. There are times when that works pretty well. If you want to see a really cool video of a bubble plot, as these are called, check out Hans Rosling talking about what's now called the Gapminder data set. He's looking at various economic data on X and Y and he then shape sizes the point by some other variable and he animates it, right? So he's got like four things going on. But there's enough differentiation in the size of the points that it really helps make the point strongly. So I think sizing mapping a variable to the size works well when you have large variation or large differentiation, I should say, in the data. But when you've got, you know, small variation between points like we see here, small amount of differentiation, it just it just doesn't work very well. It looks cool, maybe. But then when you step back and say, well, what does that mean? I don't know. Right. Anyway, well, if you find this stuff interesting and you want to dig into it more, certainly give this a thumbs up that will inspire me to keep going on. Be sure you subscribe so you see the next videos that come out. But also, if you want a more systematic look at how to work with microbiome data within R using the tidyverse, by all means, head over to rifomonas.org slash minimal R. There's a link down below in the notes, and I have a full tutorial that I use to teach my three day workshops that's up there for free for anyone to use. And I really think you can learn a lot of great basics about using the tidyverse to better understand microbiome data. Well, I hope you've been practicing and trying to incorporate these ideas with your own research. By all means, let me know if you have any questions or ideas. If there are plots out there in the wild that you would like me to take a look at and give you my feedback on what I like, what I don't like, you know, perhaps you could try to recreate it or even make it better. Let me know. I would love to have that be part of our dialogue of what we're doing here on these episodes. Well, please tell your friends about these episodes and we'll see you next time for another episode.


What did we learn from all this? So I think straight epistemology is a really incredible tool to have good conversations with people who may not necessarily agree with you or who do agree with you, but for at least both of you guys have a fair and a biased approach to assess how you reach your conclusions and whether or not the methods that you're using reach your conclusions are reliable or not. It can be done with one people or one person to be done on groups of people and it's a really fantastic way to avoid closing down people into the methodologies or their dogmen and not being willing to open up and consider how they reach their conclusions. There's a quote on that I read that I can't really remember from Facebook that basically says one of the things we can't talk about or like the whole things we can't talk about is like money, politics, or religion, but it's not because of those subjects or taboos, it's just because we don't have an effective way to have those kinds of conversations and no one really knows how to have that. And the only reason why I disagree with that comment now is because I think that we do have a method to have those kinds of conversations. I think straight epistemology can empower all of us to have a really good way to get through to people who have these walls that are set up between them and to break down that wall and actually have effective communications with people about anything. Okay, so again my name is Tyrone Wells. I believe or I'm working on a way that I can talk to anyone about anything and I think you guys can too. I think we all can. Thank you.