error need finite xlim during plotting scatter 3d for 3 axis

I am trying to plot scatter 3d plot for 3 axis. I used package:

library(scatterplot3d)

and this my dataframe:

dput(gene)
structure(list(rsid = c("geneid1", "geneid2", "geneid3", "geneid4", 
"geneid5", "geneid6", "geneid7", "geneid8", "geneid9", "geneid10", 
"geneid11", "geneid12", "geneid13", "geneid14", "geneid15", "geneid16", 
"geneid17", "geneid18", "geneid19", "geneid20", "geneid21", "geneid22", 
"geneid23", "geneid24", "geneid25", "geneid26", "geneid27", "geneid28", 
"geneid29", "geneid30", "geneid31", "geneid32", "geneid33", "geneid34", 
"geneid35", "geneid36", "geneid37", "geneid38", "geneid39", "geneid40", 
"geneid41", "geneid42", "geneid43", "geneid44", "geneid45", "geneid46", 
"geneid47", "geneid48", "geneid49", "geneid50", "geneid51", "geneid52", 
"geneid53", "geneid54", "geneid55", "geneid56", "geneid57", "geneid58", 
"geneid59", "geneid60", "geneid61", "geneid62", "geneid63", "geneid64", 
"geneid65", "geneid66", "geneid67", "geneid68", "geneid69", "geneid70", 
"geneid71", "geneid72", "geneid73", "geneid74", "geneid75", "geneid76", 
"geneid77", "geneid78", "geneid79", "geneid80", "geneid81", "geneid82", 
"geneid83", "geneid84", "geneid85", "geneid86", "geneid87", "geneid88", 
"geneid89", "geneid90", "geneid91", "geneid92", "geneid93", "geneid94", 
"geneid95", "geneid96", "geneid97", "geneid98", "geneid99", "geneid100", 
"geneid101", "geneid102", "geneid103", "geneid104", "geneid105", 
"geneid106", "geneid107", "geneid108", "geneid109", "geneid110", 
"geneid111", "geneid112", "geneid113", "geneid114", "geneid115", 
"geneid116", "geneid117", "geneid118", "geneid119", "geneid120", 
"geneid121", "geneid122", "geneid123", "geneid124", "geneid125", 
"geneid126", "geneid127", "geneid128"), empiricalpvalue = c(6.13461252366445e-122, 
1.16535620114822e-84, 8.70333130656012e-95, 6.21764431355086e-78, 
1.3419299160444e-104, 2.1205949537435e-87, 8.88049533513058e-82, 
2.37291630796694e-59, 6.89525879641339e-87, 9.15023133356126e-110, 
3.38640359272591e-95, 6.46902643155203e-97, 4.03813386099403e-68, 
9.02172515192496e-79, 1.49057561236869e-76, 3.75651498115438e-71, 
1.21242518225615e-92, 3.80900176762236e-112, 3.19156461606367e-90, 
3.12205363999601e-112, 3.75219679463562e-76, 5.79336944438183e-102, 
1.16088756611029e-92, 4.79478718145423e-71, 4.46873500738817e-68, 
3.61567839124827e-90, 2.73461291112396e-50, 5.31076204704237e-82, 
4.78173518650222e-71, 1.47603869715026e-76, 5.31076204704237e-82, 
1.34296126323826e-104, 1.47603869715026e-76, 4.78173518650222e-71, 
4.18664557737661e-102, 1.23726835252678e-47, 1.81409531313344e-87, 
1.81409531313344e-87, 9.17728799649733e-77, 1.14037287289173e-84, 
6.85171121323749e-115, 9.64380530301843e-85, 1.88308874461263e-97, 
4.54315679209976e-84, 1.15617930948075e-57, 2.61302778878597e-87, 
1.59617378477945e-107, 6.67041379381125e-97, 2.91012034679369e-73, 
6.42709856844799e-70, 4.77978670784383e-71, 3.73579797895449e-90, 
2.54822788576734e-84, 5.32401346280141e-82, 1.86531289438543e-87, 
1.27417263340724e-84, 8.47051451192377e-87, 1.67865103963281e-99, 
1.65173041055351e-87, 1.60318019118551e-92, 1.68953511584346e-97, 
1.61821544439548e-87, 1.64030885809042e-76, 2.58826953869118e-94, 
4.15415840174316e-102, 3.66836413482857e-90, 9.75351878266387e-85, 
2.15813794646134e-87, 5.20166809636258e-98, 1.45040537115182e-92, 
3.92026467069203e-76, 7.02257254289247e-80, 7.88167077050651e-100, 
5.98528923250908e-89, 2.6123159641609e-65, 4.58668502343678e-72, 
3.3269638981147e-65, 3.93215270864855e-88, 4.94770292217309e-90, 
2.61051540730913e-93, 4.82058308970484e-65, 4.03813386099403e-68, 
4.9040562801298e-68, 1.64625360058074e-97, 1.18180478789365e-67, 
2.37606653980273e-95, 6.68678557257316e-115, 2.83305168489427e-76, 
4.47438785926932e-84, 7.83381751772824e-100, 2.56336302630105e-62, 
1.6645346622893e-97, 1.49294643386617e-92, 1.30971986837447e-76, 
2.68991872345451e-62, 4.63183258997433e-71, 1.88138224471355e-97, 
1.81344406130667e-38, 4.50067096666545e-95, 1.28960110233455e-87, 
8.39303827966421e-74, 1.75361636514329e-50, 4.36558718606554e-95, 
4.23200952395284e-82, 1.77477358560346e-79, 4.4667933690595e-79, 
7.00055719563781e-82, 1.31125522310481e-87, 2.7358859862243e-56, 
7.98709105347624e-100, 1.15689932217416e-83, 3.17870997682453e-90, 
2.5665694961431e-62, 1.06323967424683e-84, 4.9588998029082e-95, 
1.73555014818939e-112, 4.76922555104304e-82, 1.29059454331569e-87, 
2.88582096884338e-92, 7.486055585569e-85, 4.43940003277464e-67, 
8.11453165153395e-107, 3.79101954373641e-76, 2.067304055207e-101, 
3.147003601088e-75, 2.3221340846221e-114, 7.49267907095058e-105, 
2.84518694290315e-52), pvalue = c(0.68588704183079, 0.68588704183079, 
0.220127260333427, 0.69423733480229, 0.490693614490964, 0.549166912433013, 
0.321119909131389, 0.470400199588203, 0.11068697727484, 0.492304167343793, 
0.977843368740407, 0.773842773679014, 0.0274086629991561, 0.0345100898198675, 
0.156009865827704, 0.177229984361821, 0.00334568549642378, 0.0246216153164539, 
0.00070484993149725, 0.00339864494961824, 0.00095625626066833, 
0.542502183036992, 0.0115397045957251, 0.0115397045957251, 0.318141606666907, 
0.00764434227225787, 0.00088342793282982, 0.00764434227225787, 
0.00764434227225787, 0.00764434227225787, 0.00764434227225787, 
0.00764434227225787, 0.00764434227225787, 0.00764434227225787, 
0.00764434227225787, 0.00764434227225787, 0.00764434227225787, 
0.00764434227225787, 0.227553616807578, 0.00307816889794103, 
0.810397696543416, 0.00481535382790678, 0.00481535382790678, 
0.567426075472232, 0.0709536216660615, 0.388300338453881, 0.723454085678846, 
0.17440795565029, 0.566179572879549, 0.0956525104821812, 0.104465873612382, 
0.702561306710734, 0.0976196418847593, 0.106833472632844, 0.106833472632844, 
0.399547088387142, 0.859507690578278, 0.0896054864434418, 0.0197881057481875, 
0.674477409919487, 0.893368122468456, 0.259198799140294, 0.0078277208585352, 
0.00660445466557924, 8.93935575744768e-07, 8.93935575744768e-07, 
0.0215191532899952, 0.00089969281273726, 1.71318094466417e-11, 
1.93744902020634e-06, 0.196919576816204, 0.00026308488486724, 
0.188048768850889, 3.37730930462203e-06, 1.71497115213503e-06, 
1.95606081221237e-09, 0.0215191532899952, 0.344393628448912, 
1.10524547799898e-06, 0.0002118690694374, 0.230805625978978, 
0.312040934992537, 0.950614873380497, 0.973950437945092, 0.154323417882195, 
0.78229924581066, 0.0197898099613507, 0.126150764855425, 0.0140779029458078, 
0.0451687447107746, 0.0451687447107746, 0.32952913111269, 0.933231564503113, 
0.318911210914388, 0.0508011296179234, 0.0435980949615047, 0.0435980949615047, 
0.0150579714577512, 0.0788408082086297, 0.0697326429444134, 0.355093197783839, 
0.191699208310582, 0.355093197783839, 0.107475347310097, 0.319442636540046, 
0.499040970288875, 0.289895623821287, 0.289895623821287, 0.0715147992163933, 
0.0823680777596502, 0.0435914001980873, 0.238698857794745, 0.238698857794745, 
0.238698857794745, 0.238698857794745, 0.032954479808064, 0.14377893219712, 
0.0957562786854422, 0.0957562786854422, 0.0957562786854422, 0.382084461781353, 
0.2559848955185, 0.183032024396735, 0.0344081978664664, 0.383607993152143, 
0.269176925197184, 0.0809293638661076, 0.0648895903300949), maxR2 = c(1, 
1, 0.24646074832345, 0.318529494648516, 0.537361473230975, 0.487775682828868, 
0.487775682828868, 0.537361473230975, 0.318529494648516, 0.195526010871951, 
0.144411290687557, 0.42495871885722, 0.42495871885722, 0.688343016856399, 
0.852092352092352, 0.688343016856399, 0.822846645483939, 0.822846645483939, 
0.92467673120711, 0.92467673120711, 0.133336040413401, 0.241614449882966, 
1, 1, 0.222225540135554, 1, 0.338767571798379, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 0.852092352092352, 0.81589109807783, 0.247206550359501, 
1, 1, 0.298914213604681, 0.269548068682413, 0.359274829666961, 
0.597926514989907, 0.597926514989907, 0.359274829666961, 0.14706412437914, 
0.365428598598603, 0.385, 0.520124160669906, 1, 1, 0.239520969186289, 
0.118172253993026, 0.246651718484139, 0.203669029422643, 0.239822084968639, 
0.224561807135871, 0.219837685176587, 0.355308267456096, 0.352300297299731, 
1, 1, 1, 0.69144988013248, 0.870624894382649, 0.71474839040327, 
0.126707938714564, 0.68463075898378, 0.239822084968639, 0.971008312455224, 
0.971008312455224, 0.870624894382649, 1, 0.173965505954282, 0.634715421497106, 
0.663625095509327, 0.173154748259788, 0.777646647937935, 0.777646647937935, 
0.494829318691275, 0.669948731345372, 0.286608298357456, 0.669948731345372, 
0.257854250390985, 0.239520969186289, 1, 1, 0.191448862824438, 
0.184880399183239, 0.160153297583809, 0.98254847816179, 1, 1, 
0.940413080805106, 0.571737457140003, 0.940413080805106, 1, 0.162156384275673, 
1, 0.243533199479121, 0.155160539315454, 0.671263122385402, 1, 
1, 0.205198409129552, 0.210437753515572, 0.189411423519086, 1, 
1, 1, 1, 0.296376406781993, 0.923490988913509, 1, 1, 1, 0.241614449882966, 
0.169138820306718, 0.148054212558727, 0.223841261627209, 0.167433583712982, 
0.262610336629144, 0.385, 0.20449643660452)), row.names = c(NA, 
-128L), class = c("tbl_df", "tbl", "data.frame"))

When I run this code it gives me an error:

scatterplot3d(gene$pvalue,gene$empiricalpvalue, gene$maxR2)
Error in plot.window(c(x1, x2), c(z.min, z.max + yz.f * y.max), asp = asp) : 
  need finite 'xlim' values

I checked this particular error in google and it corresponds to having NA values in dataframe but In my case I don't have any NA values. I have added my entire dataset for reference. Is there any way to solve this issue or any other package for plotting 3d scatter plot. Thank you.

Solution

All your empirical p values are very small:

range(gene$empiricalpvalue)
#> [1] 6.134613e-122  1.813444e-38

The code inside scatterplot3D takes this range, converts it into a sequence of pretty breaks, then takes the difference between the first two breaks as the scaling factor for the y axis. Unfortunately, it rounds this scaling factor to 12 decimal places. This all happens in the lines:

y.prty <- pretty(y.range, n = lab[2], 
                 min.n = max(1, min(0.5 * lab[2], p.lab[2])))
y.scal <- round(diff(y.prty[1:2]), digits = 12)

Since your scaling factor is about 10^-39, rounding it to 12 decimal places rounds it down to 0. When the y values are scaled for plotting, they are therefore divided by 0. This makes them all Inf, so when the lower level graphic functions try to plot them, there are no finite values to plot.

If you take the log of your p values, this problem disappears:

scatterplot3d(log10(gene$pvalue), log10(gene$empiricalpvalue), gene$maxR2)