# Make 3d scatter plot with data on vegetation

Hi Community,
I want to do a 3d scatter plot of the following information. The variables are x: Ground roughness ; y : roughness index ; z = probability of presence of vegetation .

I want to show that when the roughness is greater there is a greater probability of vegetation.

In an article I found this graphic and I would like to replicate it:

Im try whit different options but not work well.
1

library(plotly)
x = R\$lyr17_vm_vector_ruggedness
y = R\$lyr17_vm_TRI
z = R\$lyr17_veg_map_sp_holdout_probability.2

plot_ly(R, x = x, y = y, z = z,
type = 'scatter3d',
mode = 'line',
opacity = 7)

2

require(rgl)
with(R,plot3d(x,y,z,
type = "s",
opacity = 1,
col = c("red","blue","green")))

3

library(plot3D)
library(plot3Drgl)
with(R,scatter3D(x,y,z,
ticktype="detailed",
type= "s",
pch=16,
xlab="vector_ruggedness",
ylab="TRI",
main=""))
plotrgl(lighting = TRUE, smooth = TRUE, cex=2)

Im make other examples but is wrong.
I consider that I have problems in returning matrix to z Dont know how to make well.

Thanks

dput(R[1:500,2:4]) structure(list(lyr17_veg_map_sp_holdout_probability.2 = c(0.444000006,  0.526000023, 0.660000026, 0.54400003, 0.649999976, 0.621999979,  0.477999985, 0.684000015, 0.572000027, 0.574000001, 0.453999996,  0.469999999, 0.582000017, 0.614000022, 0.515999973, 0.68599999,  0.617999971, 0.505999982, 0.453999996, 0.414000005, 0.550000012,  0.474000007, 0.442000002, 0.628000021, 0.702000022, 0.688000023,  0.628000021, 0.540000021, 0.565999985, 0.717999995, 0.666000009,  0.536000013, 0.493999988, 0.405999988, 0.634000003, 0.578000009,  0.639999986, 0.593999982, 0.518000007, 0.638000011, 0.629999995,  0.737999976, 0.635999978, 0.662, 0.479999989, 0.578000009, 0.574000001,  0.628000021, 0.492000014, 0.409999996, 0.698000014, 0.65200001,  0.667999983, 0.488000005, 0.681999981, 0.601999998, 0.657999992,  0.565999985, 0.59799999, 0.469999999, 0.674000025, 0.70599997,  0.653999984, 0.569999993, 0.404000014, 0.768000007, 0.694000006,  0.589999974, 0.666000009, 0.653999984, 0.660000026, 0.453999996,  0.560000002, 0.5, 0.596000016, 0.574000001, 0.624000013, 0.589999974,  0.558000028, 0.526000023, 0.653999984, 0.723999977, 0.666000009,  0.638000011, 0.730000019, 0.526000023, 0.505999982, 0.572000027,  0.634000003, 0.660000026, 0.69599998, 0.527999997, 0.727999985,  0.432000011, 0.628000021, 0.75, 0.758000016, 0.653999984, 0.606000006,  0.523999989, 0.375999987, 0.601999998, 0.488000005, 0.505999982,  0.712000012, 0.648000002, 0.629999995, 0.589999974, 0.55400002,  0.667999983, 0.632000029, 0.603999972, 0.589999974, 0.632000029,  0.526000023, 0.430000007, 0.286000013, 0.432000011, 0.726000011,  0.568000019, 0.635999978, 0.526000023, 0.361999989, 0.560000002,  0.635999978, 0.463999987, 0.671999991, 0.615999997, 0.342000008,  0.568000019, 0.593999982, 0.465999991, 0.463999987, 0.469999999,  0.65200001, 0.777999997, 0.555999994, 0.646000028, 0.722000003,  0.675999999, 0.5, 0.532000005, 0.579999983, 0.666000009, 0.519999981,  0.579999983, 0.501999974, 0.458000004, 0.34799999, 0.606000006,  0.588, 0.745999992, 0.75, 0.621999979, 0.731999993, 0.589999974,  0.550000012, 0.648000002, 0.667999983, 0.763999999, 0.643999994,  0.70599997, 0.442000002, 0.493999988, 0.501999974, 0.479999989,  0.419999987, 0.451999992, 0.680000007, 0.657999992, 0.703999996,  0.741999984, 0.634000003, 0.723999977, 0.779999971, 0.69599998,  0.811999977, 0.663999975, 0.68599999, 0.80400002, 0.379999995,  0.349999994, 0.493999988, 0.460000008, 0.495999992, 0.639999986,  0.629999995, 0.560000002, 0.726000011, 0.765999973, 0.762000024,  0.680000007, 0.574000001, 0.69599998, 0.702000022, 0.629999995,  0.555999994, 0.702000022, 0.674000025, 0.345999986, 0.533999979,  0.55400002, 0.5, 0.628000021, 0.574000001, 0.681999981, 0.698000014,  0.787999988, 0.657999992, 0.731999993, 0.629999995, 0.603999972,  0.523999989, 0.492000014, 0.497999996, 0.526000023, 0.702000022,  0.505999982, 0.331999987, 0.600000024, 0.453999996, 0.458000004,  0.497999996, 0.629999995, 0.600000024, 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0.479999989, 0.532000005, 0.428000003, 0.492000014,  0.398000002, 0.377999991, 0.560000002, 0.512000024, 0.50999999,  0.474000007, 0.467999995, 0.529999971, 0.463999987, 0.512000024,  0.532000005, 0.492000014, 0.513999999, 0.49000001, 0.505999982,  0.512000024, 0.523999989, 0.638000011, 0.476000011, 0.55400002,  0.639999986, 0.703999996, 0.603999972, 0.495999992, 0.428000003,  0.444000006, 0.433999985, 0.409999996, 0.474000007, 0.307999998,  0.384000003, 0.522000015, 0.508000016, 0.508000016, 0.481999993,  0.519999981, 0.50999999, 0.533999979, 0.596000016, 0.439999998,  0.35800001, 0.56400001, 0.561999977, 0.412, 0.55400002, 0.574000001,  0.56400001, 0.772000015, 0.437999994, 0.316000015, 0.49000001,  0.363999993, 0.483999997, 0.5, 0.305999994, 0.469999999, 0.541999996,  0.536000013, 0.518000007, 0.649999976, 0.50999999, 0.49000001,  0.497999996, 0.513999999, 0.453999996, 0.5, 0.625999987, 0.469999999,  0.558000028, 0.582000017, 0.583999991, 0.586000025, 0.786000013,  0.421999991, 0.593999982, 0.532000005, 0.540000021, 0.495999992,  0.59799999, 0.495999992, 0.523999989, 0.497999996, 0.472000003,  0.529999971, 0.536000013, 0.55400002, 0.5, 0.5, 0.533999979,  0.467999995, 0.565999985, 0.55400002, 0.615999997, 0.44600001,  0.522000015, 0.698000014, 0.526000023, 0.550000012, 0.54400003,  0.372000009, 0.407999992, 0.493999988, 0.611999989, 0.610000014,  0.519999981, 0.409999996, 0.546000004, 0.635999978, 0.550000012,  0.540000021, 0.555999994, 0.572000027, 0.586000025, 0.561999977,  0.55400002, 0.512000024, 0.54400003), lyr17_vm_TRI = c(1.018741608,  1.898422241, 1.59016037, 0.731349945, 0.506702423, 0.669364929,  0.983158112, 1.460777283, 1.126293182, 1.096321106, 1.68523407,  1.212741852, 0.398029327, 0.609077454, 0.85824585, 0.693790436,  1.378501892, 1.33927536, 1.13615036, 1.466972351, 1.004394531,  0.862640381, 1.114643097, 1.027637482, 0.751846313, 1.184238434,  1.429821014, 1.009338379, 0.57976532, 0.271396637, 0.403427124,  1.369628906, 1.149318695, 1.03086853, 0.937942505, 1.435035706,  1.374069214, 0.960483551, 1.354122162, 1.446735382, 0.745578766,  0.416069031, 0.356632233, 0.50120163, 1.262271881, 0.793346405,  0.804481506, 0.750488281, 1.220420837, 1.661140442, 0.884616852,  1.127254486, 1.313694, 1.111995697, 0.453170776, 0.513019562,  0.706298828, 1.064720154, 1.015323639, 0.75447464, 0.477481842,  0.584999084, 1.034420013, 1.195129395, 1.336235046, 1.002925873,  0.989738464, 0.534740448, 0.399044037, 0.44776535, 0.662437439,  1.600547791, 1.143844604, 1.155422211, 0.786727905, 0.985721588,  0.673664093, 1.068153381, 1.34771347, 1.060649872, 0.689170837,  0.557579041, 0.461349487, 0.492050171, 0.607738495, 1.075534821,  1.265277863, 1.723560333, 1.265346527, 1.139835358, 0.984230042,  1.036460876, 1.149250031, 1.20489502, 0.848018646, 0.647041321,  0.501888275, 0.45167923, 0.51505661, 0.76524353, 1.635704041,  1.834812164, 0.991443634, 0.829597473, 0.928245544, 0.837615967,  1.114578247, 1.535419464, 1.116176605, 0.718883514, 0.398609161,  0.368656158, 0.505146027, 0.855762482, 2.746429443, 1.801544189,  2.178859711, 1.591712952, 0.520202637, 0.864467621, 0.909881592,  0.961288452, 1.448471069, 1.449085236, 1.345630646, 1.035968781,  0.660881042, 0.701457977, 1.412509918, 1.089817047, 2.800983429,  2.366405487, 1.894313812, 1.659912109, 0.908740997, 0.867977142,  0.852657318, 0.765274048, 0.97756958, 1.071247101, 1.21005249,  0.785125732, 0.501960754, 0.866687775, 0.938854218, 0.853591919,  3.071552277, 2.017780304, 1.85062027, 1.81496048, 1.235298157,  0.884506226, 0.767505646, 0.643749237, 0.723972321, 1.035049438,  1.003635406, 0.468448639, 0.381969452, 0.454650879, 0.484069824,  0.558517456, 2.476306915, 3.260692596, 3.822223663, 2.32844162,  1.668956757, 2.042285919, 1.30406189, 1.135429382, 0.790035248,  0.7147789, 0.872447968, 0.9376297, 0.87361145, 0.724746704, 0.495967865,  0.482822418, 0.503890991, 0.709716797, 1.710041046, 3.108547211,  4.195171356, 2.983688354, 1.638523102, 1.655479431, 1.028663635,  1.003376007, 0.933280945, 0.898086548, 0.984725952, 0.94291687,  0.814208984, 0.799678802, 0.764011383, 0.732479095, 0.694892883,  0.756782532, 1.181797028, 2.3618927, 3.678195953, 3.885684967,  2.268352509, 1.208065033, 0.927032471, 0.745033264, 0.905986786,  0.977867126, 0.92339325, 0.768386841, 0.673442841, 0.616085052,  0.692630768, 0.556179047, 0.526767731, 0.610076904, 0.919200897,  1.051971436, 2.225711823, 2.98204422, 3.763526917, 3.292961121,  1.627773285, 1.227233887, 0.833679199, 0.896091461, 0.924385071,  0.83158493, 0.570419312, 0.309986115, 0.362869263, 0.532234192,  0.667201996, 0.598529816, 0.527511597, 1.025745392, 1.250137329,  2.083438873, 2.226039886, 2.98758316, 3.831375122, 2.304676056,  1.598968506, 0.896408081, 0.704219818, 0.704040527, 0.779418945,  0.407752991, 0.329410553, 0.521816254, 1.028964996, 0.766605377,  0.448436737, 0.380558014, 0.995109558, 1.347930908, 2.397281647,  2.018135071, 2.057533264, 3.922538757, 3.424125671, 1.421672821,  1.069171906, 0.65769577, 1.219631195, 0.464572906, 0.360229492,  0.43466568, 0.826747894, 0.808917999, 0.710231781, 0.38237381,  0.179710388, 1.261623383, 1.84563446, 2.204200745, 1.629238129,  1.75736618, 3.919967651, 3.588760376, 1.443916321, 1.052619934,  0.880561829, 1.035747528, 0.750312805, 0.518611908, 0.437175751,  1.220333099, 0.663105011, 1.006580353, 0.291374207, 0.134296417,  2.089763641, 2.167877197, 1.733707428, 1.339889526, 1.710681915,  3.932086945, 3.521408081, 1.619419098, 1.210838318, 1.202003479,  0.94140625, 1.136940002, 0.696346283, 0.677288055, 0.937164307,  0.641326904, 0.402362823, 0.370429993, 0.21818924, 2.509746552,  2.291431427, 1.784393311, 1.947784424, 2.529045105, 4.088554382,  2.961532593, 1.42382431, 1.118663788, 0.759174347, 0.722110748,  1.126731873, 0.936168671, 1.194610596, 0.654491425, 0.289043427,  0.240642548, 0.2302742, 0.314571381, 0.524147034, 0.678447723,  2.323154449, 1.764183044, 1.956680298, 2.221801758, 2.386234283,  3.731349945, 2.559436798, 0.907123566, 1.181762695, 0.809467316,  0.802585602, 0.920021057, 1.179386139, 0.701972961, 0.435043335,  0.185966492, 0.37140274, 0.182273865, 0.338039398, 0.510139465,  0.467704773, 1.384929657, 1.616153717, 1.349151611, 1.203327179,  1.609409332, 1.791679382, 1.372730255, 2.61265564, 3.419399261,  1.454673767, 1.242126465, 0.995800018, 0.889923096, 0.809280396,  0.43768692, 0.389884949, 0.148433685, 0.177898407, 0.347381592,  0.402141571, 0.341464996, 0.421333313, 0.391170502, 1.26083374,  1.153381348, 1.029735565, 0.993606567, 1.314128876, 1.554416656,  1.716487885, 3.106170654, 3.67987442, 2.152709961, 1.8891716,  2.162296295, 1.473754883, 0.568843842, 0.229934692, 0.322166443,  0.291629791, 0.251804352, 0.225585938, 0.186351776, 0.30513382,  0.414344788, 0.396446228, 1.653781891, 1.323532104, 1.025489807,  0.703006744, 0.941101074, 0.866439819, 0.933078766, 1.097328186,  2.476940155, 3.682186127, 2.933578491, 2.751247406, 2.484695435,  2.570949554, 1.827331543, 0.477508545, 0.234695435, 0.332164764,  0.463245392, 0.293151855, 0.187232971, 0.149044037, 0.435962677,  0.442100525, 0.254619598, 1.403308868, 1.201591492, 0.625080109,  0.522144318, 0.764003754, 0.785140991, 0.638076782, 1.397808075,  2.8697052, 2.744384766, 1.839473724, 1.429767609, 1.351127625,  1.985466003, 1.036567688, 0.517093658, 0.234794617, 0.456771851,  0.417778015, 0.307197571, 0.235977173, 0.12040329, 0.321208954,  0.482318878, 0.266475677, 1.268669128, 0.949634552, 0.481056213,  0.286247253, 0.681091309, 0.848304749, 0.464828491, 1.083332062,  2.859806061, 2.70640564, 1.235118866, 0.811710358, 0.734249115,  0.738697052, 0.479804993, 0.171596527, 0.472724915, 0.577045441,  0.388877869, 0.268863678, 0.245243073, 0.26316452, 0.287784576,  0.459064484, 0.283363342, 1.499629974, 0.9388237, 0.979885101,  0.558818817, 0.441280365, 0.698894501, 0.839004517, 0.75750351,  1.794662476, 2.579200745, 2.173908234, 1.321983337, 0.620326996,  0.559841156, 0.827880859, 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3.691925049, 3.728424072, 2.863372803,  3.496948242, 1.846862793, 1.335693359, 1.505645752, 2.426635742,  4.313903809, 4.736572266, 3.485870361, 3.102752686, 2.045471191,  2.31427002, 3.691925049, 3.931427002, 3.127655029, 2.722381592,  2.20022583, 1.740692139, 1.96963501, 1.499053955, 3.790161133,  5.059448242, 5.087677002, 3.458709717, 3.458709717, 3.318634033,  2.443572998, 3.931427002, 3.127655029, 3.299072266, 1.863433838,  1.79586792, 1.468475342, 1.329071045, 3.020324707, 4.016967773,  4.441680908, 2.142333984, 2.903289795, 3.38482666, 3.147186279,  4.234008789, 3.621185303, 4.334136963, 2.737945557, 1.786804199,  1.068359375, 2.390228271, 3.218994141, 9.093200684, 5.455841064,  3.961273193, 4.752929688, 2.060638428, 2.376525879, 2.417144775,  2.525817871, 3.530761719, 4.942901611, 4.60925293, 3.013061523,  1.348480225, 2.163330078, 3.029907227, 3.744598389, 8.399261475,  6.31048584, 5.130493164, 5.741546631, 2.965820313, 2.761871338,  3.499053955, 2.740692139, 3.11114502, 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Hi @M_AcostaCH,
You may have already solved your 3D surface plotting issue. If not, this plot_ly example may help:

suppressPackageStartupMessages(library(plotly))

# Use a small subset of the original data (first 10 rows)
mydata <- structure(list(x = c(0.444000006, 0.526000023, 0.660000026, 0.54400003,
0.649999976, 0.621999979, 0.477999985, 0.684000015, 0.572000027,
0.574000001), y = c(1.018741608, 1.898422241, 1.59016037, 0.731349945,
0.506702423, 0.669364929, 0.983158112, 1.460777283, 1.126293182,
1.096321106), z = c(2.988586426, 5.521240234, 5.039703369, 1.889678955,
2.008758545, 2.324188232, 2.321990967, 4.444793701, 3.836914063,
3.175598145)), class = "data.frame", row.names = c(NA, -10L))

# For add_surface(), z values must be in diagonal matrix to match the x,y coordinates
zz <- diag(mydata\$z, nrow=length(mydata\$z), ncol=length(mydata\$z))

p1 <- plot_ly(mydata, x=~x, y=~y)  # Defaults to x~y scatterplot
p2 <- add_surface(p1, z=zz)    # surface layer will be much smoother with many points
p2
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@DavoWW tnks. Im try to make this maybe for 1 year ago. Im try and try but can't make it.

Run with the full data, and this the result:

Really many thanks for you

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