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I am making a 3D scatterplot (image attached) of principal components. Although I'm using aspectmode='cube', the axes are not equal in size.

enter image description here

I created an MRE to test, and in that test, the axes to come out equal. So, I'm very confused.

axx <- list(
  gridcolor='rgb(255, 255, 255)',
  zerolinecolor='rgb(255, 255, 255)',
  showbackground=TRUE,
  backgroundcolor='rgb(230, 230,230)'
)

df = data.frame(
  X=rnorm(100, mean=-5, sd=2),
  Y=rnorm(100, mean=5, sd=5),
  Z=rnorm(100, mean=20, sd=10),
  color=sample(c('R','G'), 100, replace = T)
)

plot_ly(
  data=df, 
  x = ~X, 
  y = ~Y, 
  z = ~Z, 
  color=~color
  ) %>%
  add_markers(size=3) %>%
  # layout(autosize = F, width = 1000, height = 1000)
  layout(
    # autosize=F,
    # width=700,
    # height=700,
    aspectmode='cube',
    title = 'MiSeq-239 Principal Components',
    scene = list(xaxis=axx, yaxis=axx, zaxis=axx),
    paper_bgcolor = 'rgb(243, 243, 243)',
    plot_bgcolor = 'rgb(243, 243, 243)'
    )

enter image description here

Real Data

df = data.frame(
  PC1=c(0.402285144003261,1.4171695209575,-0.636749686422501,2.25024242477446,-0.841449299879213,-0.814419884751789,2.07378541014841,-0.778655366569915,-0.270510046040042,1.93710878668601,-0.204151727584088,1.18675386419666,-1.15183163106794,-0.93729638809887,-0.302710575107095,-1.09505445967183,-1.21552773114306,0.413320681421469,1.33687147572696,0.407904518638843,-0.779028649942894,-1.33696908904798,-0.233015236454913,0.35225066203097,1.6253605258001,1.38908779425315,-0.825671237656062,-0.560424988418219,0.651203145837364,2.058167645016,1.14526323821716,2.00625493277667,-0.0738636435202872,-0.284276158583548,2.18298399877386,-1.24082057644767,-1.22427038717449,-0.797599236553793,-0.644062745636431,0.626727844681026,1.98405367505224,-0.30069951949164,-1.23719135962738,1.43043331347688,0.116338609902778,-1.20787242688613,-0.675116638900054,-0.755292892588987,-1.25329048584962,-0.338781457022259,-0.107165383056406,-0.640496143088783,-0.853495558358877,-1.13400491664111,-0.425905080519206,0.314948307010327,-0.176343304604597,0.812600292304552,-0.689807236191771,-0.107039622042221,-0.505836714238656,-1.236739303571,-0.19463981358001,-0.916245478804557,3.33272908429981,0.0608810071077068,0.320806980146676,-1.43672309252606,-0.872334924217026,2.93800267031722,1.74331480788324,-0.127481839044974,1.10232163273596,-1.18053517163663,-0.583944280435473,2.91279366730135,-0.79411540469038,-1.34695953634993,0.84421649882345,-0.399359269417906,-0.524386948445777,-0.864372867873221,-1.4513340499215,-1.19440393237087,-0.727719334458475,-0.383382463796734,0.984901156287103,-0.762592307336777,0.452913567561011,0.821307331892765,0.438220819724908,0.0168627531475347,1.90134990281157,-0.457595439918553,0.674440080100837,1.80700544468329,1.44766526949108,1.87218759733718,-0.675225790428008,-1.01446164695057,-0.839626836802754,-0.87440205023598,-1.29255224846617,-0.403915576623382,-1.15071619104369,-0.451329811450679,0.161765738564826,-0.530973567290627,-1.52897735513236,0.795290275200284,-1.09618873783387,-1.23811553857377,-0.818092480976885,0.419682383341886,0.118566391474338,2.29655580176131,-0.727237776009522,-0.38818997901355,0.609446493322166,-0.661480237880466,0.368594401718748,-1.075975628103,0.963234802514334,-1.19133091075783,-0.971765389994952,2.95651190409003,-0.446829002191232,-0.743097737525159,-0.709478214011909,-0.853724528400848,-1.0953870682951,-1.15841828790577,-1.05708487979213,4.62345613963919),
  PC2=c(-0.691442417923578,-0.683079840989716,-0.508805612645602,0.310124183701145,-0.333359912443457,-0.800693619112235,0.085202920424396,-0.11132735865037,-0.666403768217729,-0.0834748188236059,-0.345047196968817,0.17842154902598,-0.639680797448222,0.461583332814334,-0.535599436330943,0.0237661360475331,0.398227929480799,-0.473097275114053,-0.407826836179771,-0.787460273256553,-0.632110095458283,0.293036356935143,-0.0261353332247592,1.74508155429367,0.173506020900256,-0.197903882583297,0.216078539613414,-0.120045617632566,-0.435771015868879,0.0587322085417543,-0.458026351200192,0.522310573056916,-0.751249128576159,-0.681622222714507,-0.0119462713603535,0.186349913516978,-0.073365944613263,-0.703357642739476,-0.762586386300058,-0.390827630338644,-0.159399980975471,-0.64942816302922,0.362640302315422,-0.343569418769015,0.00940186847067734,-0.307033450665064,-0.284026380841206,0.0848178676708685,0.145461952525289,0.0445692166880105,-0.479639339732628,0.497067063401757,-0.624634242815239,0.198201574580486,1.03586534103812,-0.695901741788024,-0.495076850381257,-0.159202416957294,0.508387562014729,-0.801904864319242,-0.352887593201084,-0.0979899399649464,0.661204492559326,-0.0353074276609244,0.793422871975105,-0.837102754131842,-0.387244804124702,0.379950022326929,1.09353454995192,0.11286469697211,-0.238402512309026,1.02658415334493,-0.405737978169531,-0.319728049872764,-0.0678533793665141,0.387249596539791,-0.57289942606773,0.621224280780749,-0.757348371955016,-0.0995226548027982,1.34260621422433,0.481352595393131,0.36123875438456,0.725696031349409,0.46264920965195,1.42821849906345,-0.440278745261427,-0.540546039701434,-0.553442266651548,-0.49093139262921,-0.293637136234839,-0.733558079546156,-0.126283772731982,-0.397415357333659,-0.736779913291033,0.223387767872012,0.219747287161707,-0.280300495103552,-0.371326555673896,0.5048026973908,0.889198753971627,0.451122232620754,-0.320969768454131,-0.796093450420807,-0.31519998293736,0.164019068998799,-0.618787824472785,-0.682261924082798,0.309010097143683,-0.770450326898851,-0.378760251921075,-0.0660735214480938,0.319233322557814,-0.15103193559757,0.411678752309201,-0.0361707225437949,1.0735553496112,1.09271229042861,-0.271562559613672,-0.230226950220361,-0.463833247578663,0.454005830614009,0.3994521713863,0.521021290137487,0.372722642029952,1.03412661393332,0.952395517233731,0.746585488938323,0.860055062087748,0.988406726965946,-0.339924842387608,0.593440971150134,0.417819332457096,1.4748062887763),
  PC3=c(0.78619943941128,0.43900154655854,-0.341118402369532,0.859428973982257,0.0027538969866319,0.261614636856235,-1.34075225507253,-0.141238485773147,0.45409680961907,-0.0921369165145691,0.304349936665113,0.670621568821989,0.150090275443703,-0.00630519340032405,-0.217939897320828,0.153913785536882,-0.151732015639995,-0.413303837888523,0.866185004773742,-0.332837341137064,0.0131732954744622,-0.241394043212782,0.41729623042356,-0.0649113326022627,1.20197863235631,0.0446977387781464,-0.354665773452229,-0.181159217591208,-0.273888528930021,-1.12798196562189,0.021890039031337,0.781429491231414,0.295045553919176,-0.0215301667556246,-1.37039669616791,-0.154896374866593,-0.0834548379840878,-0.181538678547918,-0.22585394574165,-0.408738601592734,0.612695296087596,0.152460767067255,-0.062960963201121,0.832870733541891,-0.000147381698993598,-0.0440568613398221,-0.428647800180143,0.392596253920975,-0.300991629277747,0.368250962783333,0.389759121271554,-0.367875465370281,0.15015817198429,-0.263928629365438,0.488991532708951,0.468558428266446,0.0456103925023596,0.768855044247282,0.193526741310598,-0.187671320529716,0.145204422795546,0.0690238768897314,0.302764765795145,-0.139858223316948,0.549653681151185,-0.321488686998528,0.685480426634766,-0.123599715575736,0.12834181518971,0.793496681163536,-0.634720554547527,0.760197797899689,-0.906572581798678,-0.189316129740401,-0.151125605918338,-1.2993501989525,0.0602141217939274,-0.182333698555019,-0.122486801497072,0.105385601478453,0.115374511101675,0.10183779380354,-0.0701463184861918,-0.211101622848838,-0.000185233188477408,0.148300158541414,-0.0653518230584272,-0.297161719872819,-0.341509915525046,-0.033356645558132,0.242133550019011,0.855452789566318,-1.35012232845054,-0.183482091763533,0.341444834709581,-0.066324577740098,1.05960459079952,0.86894681928822,0.476121141928887,-0.193649910316473,0.14535036399593,-0.277789505804451,-0.106503050428773,-0.165814382622154,-0.183839809056858,0.443999312925312,-0.567794411136856,0.152060669939955,-0.0134495792327868,-0.416022681039047,-0.0533562830668323,-0.11240720527039,0.0946074156935571,0.318887201210059,-0.195410482573163,-0.575749169988158,-0.128882469478499,0.195748794005393,-0.170194769581065,-0.0724930628838023,-0.240345090405827,-0.133713214239894,-0.759009487448492,0.182057572862671,0.0734334340698879,-1.04537341217951,0.00939322852534254,-0.0289834688700101,-0.0139702215267289,-0.146550672852971,-0.0790048982707758,-0.163629275776705,-0.307809524158755,0.212777395408197),
  CaseString=c("AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","AMD","AMD","AMD","AMD","AMD","AMD","AMD","AMD","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","Control","AMD")
)

axx <- list(
  gridcolor='rgb(255, 255, 255)',
  zerolinecolor='rgb(255, 255, 255)',
  showbackground=TRUE,
  backgroundcolor='rgb(230, 230,230)'
)

plot_ly(
  data=df, 
  x = ~PC1, 
  y = ~PC2, 
  z = ~PC3, 
  color=~CaseString
  ) %>%
  add_markers(size=3) %>%
  # layout(autosize = F, width = 1000, height = 1000)
  layout(
    # autosize=F,
    # width=700,
    # height=700,
    aspectmode='cube',
    title = 'MiSeq-239 Principal Components',
    scene = list(xaxis=axx, yaxis=axx, zaxis=axx),
    paper_bgcolor = 'rgb(243, 243, 243)',
    plot_bgcolor = 'rgb(243, 243, 243)'
    )
faken
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abalter
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  • Can you share the example that you have problem with. Not the one that came out as what you expected. ```I created an MRE to test, and in that test, the axes to come out equal. So, I'm very confused.``` We don't need to see the "MRE" that you made for test that actually worked. We need to see a reproducible example of your problem. – M-- Sep 24 '19 at 20:22
  • I cannot. It is based on a large data set with PHI (Personal Health Information). Perhaps I could paste in just the PCoA data. – abalter Sep 24 '19 at 20:39
  • I think you are already familiar with this, but just sharing again: https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example ... without a reproducible example, it's almost impossible to help. (you may be able to remove some columns, change some names, get a subset and reproduce the problem). Otherwise, question will be closed as NO MCVE. Cheers. – M-- Sep 24 '19 at 20:44
  • Ok. Pasted in the actual data. However, IMO, "almost impossible to help" is a bit strong. I've answered tons of questions without that much information. Perhaps there is simply another switch needed in some circumstances, or a known bug, etc. Not trying to pick on you, but closing this question when I DID create a minimally reproducible counterexample, would be a bit draconian. – abalter Sep 24 '19 at 20:51

2 Answers2

1

You need to put aspectmode='cube' into the scene list, i.e.:

scene = list(xaxis=axx, 
             yaxis=axx, 
             zaxis=axx, 
             aspectmode='cube')

This is especially important if you want to animate the scene, as per this answer. Without that, the axes will wobble.

mattek
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0

My solution was by two invisible points "rgba(255, 255, 255, 0)", one with the coordinates with the highest value obtained, and the other with the coordinates with the lowest value obtained.

Successful example.

Antonio Vandré P F Gomes
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