I used the below code to do 3D PCA, all I want to make a 3D box plot.
Mydata = read.csv("PCA.csv")
head(Mydata)
pca = prcomp(Mydata[,6:11], scale. = TRUE)
summary(pca)
library(pca3d)
gr = factor(Mydata[,1])
pca3d(pca, group = gr)
dput(Mydata)
pca3d(pca,title = "Nanjing", axes.color= "black",group=gr, show.ellipses=TRUE,
ellipse.ci=0.95,biplot=TRUE, biplot.vars=3, show.centroids= TRUE,show.group.labels=FALSE, show.plane=FALSE, legend = "topleft")
To download the image I used
snapshotPCA3d(file="Nanjing.png")
but it didn't work, it is showing a warning text which I didn't understand (look below)
Warning messages: 1: In rgl.snapshot(filename = file, fmt = "png", top = TRUE) : RGL: PNG Pixmap Saver Warning: Image width is zero in IHDR 2: In rgl.snapshot(filename = file, fmt = "png", top = TRUE) : RGL: PNG Pixmap Saver Warning: Image height is zero in IHDR 3: In rgl.snapshot(filename = file, fmt = "png", top = TRUE) : RGL: PNG Pixmap Saver Error: Invalid IHDR data 4: In rgl.snapshot(filename = file, fmt = "png", top = TRUE) : RGL: PNG Pixmap Saver Error: an error occured 5: In rgl.snapshot(filename = file, fmt = "png", top = TRUE) : 'rgl.snapshot' failed
Data I used
structure(list(Location = c("Ningde Coastal Area", "Ningde Coastal Area",
"Ningde Coastal Area", "Ningde Coastal Area", "Ningde Coastal Area",
"Ningde Coastal Area", "Ningde Coastal Area", "Ningde Coastal Area",
"Ningde Coastal Area", "Ningde Coastal Area", "Ningde Coastal Area",
"Ningde Coastal Area", "Ningde Coastal Area", "Ningde Coastal Area",
"Ningde Coastal Area", "Ningde Coastal Area", "Ningde Coastal Area",
"Luoyuan Bay", "Luoyuan Bay", "Luoyuan Bay", "Luoyuan Bay", "Luoyuan Bay",
"Luoyuan Bay", "Luoyuan Bay", "Luoyuan Bay", "Luoyuan Bay", "Luoyuan Bay",
"Luoyuan Bay", "Luoyuan Bay", "Luoyuan Bay", "Luoyuan Bay", "Luoyuan Bay",
"Luoyuan Bay", "Luoyuan Bay", "Luoyuan Bay", "Luoyuan Bay", "Luoyuan Bay",
"Luoyuan Bay"), Serial = c(14L, 15L, 17L, 18L, 19L, 20L, 21L,
22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L,
35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L,
48L, 49L, 50L, 51L, 52L), Station = c("NDDZ031", "NDDZ034", "NDDZ035",
"NDDZ041", "NDDZ046", "NDDZ048", "NDDZ050", "NDDZ055", "NDDZ058",
"NDDZ065", "NDDZ066", "NDDZ068", "NDDZ072", "NDDZ073", "NDDZ074",
"NDDZ080", "NDDZ082", "NDDZ91", "NDDZ92", "NDDZ94", "NDDZ95",
"NDDZ96", "NDDZ97", "NDDZ98", "NDDZ99", "NDDZ103", "NDDZ105",
"NDDZ106", "NDDZ107", "NDDZ112", "NDDZ113", "NDDZ114", "NDDZ115",
"NDDZ116", "NDDZ117", "NDDZ119", "NDDZ122", "NDDZ123"), Longitude = c(119.8156314,
119.8109757, 119.9013884, 120.1667206, 120.0796901, 119.7829741,
119.9602213, 119.7401038, 120.1113902, 119.7060803, 120.1239972,
119.7798066, 120.0968136, 119.7086703, 119.7827459, 120.0751752,
120.0621476, 119.6875, 119.6641667, 119.7163889, 119.7425, 119.69,
119.7719444, 119.6622222, 119.7544444, 119.6644444, 119.6875,
119.7369444, 119.7672222, 119.6583333, 119.6327778, 119.5991667,
119.6769444, 119.7019444, 119.7419444, 119.6216667, 119.6722222,
119.6408333), Latitude = c(26.48095232, 26.51638163, 26.53300528,
26.54343039, 26.56656159, 26.59238665, 26.6023812, 26.62635719,
26.64614884, 26.70021888, 26.70684282, 26.72669529, 26.75513142,
26.77262578, 26.7665767, 26.82756691, 26.6238606, 26.34944444,
26.35972222, 26.36, 26.36027778, 26.37583333, 26.38277778, 26.38638889,
26.39277778, 26.41055556, 26.41972222, 26.42833333, 26.42861111,
26.43361111, 26.44416667, 26.45, 26.45, 26.44805556, 26.44805556,
26.46638889, 26.47166667, 26.4775), MPs = c(101.1310963, 126.7889088,
85.74767297, 153.5234525, 51.35979247, 42.82041038, 214.4548942,
96.9063435, 155.5864259, 46.01889546, 97.50099786, 78.36325034,
161.375366, 99.76091135, 59.82528502, 98.7524581, 110.3141717,
89.08, 103.02, 89.61, 106.42, 36.85, 66.93, 81.39, 152.58, 171.61,
105.34, 148.31, 293.68, 279.4, 248.44, 273.39, 131.06, 36.33,
29.62, 89.07, 382.31, 170.27), Petrolium = c(26.41089103, 5.575674479,
112.1713291, 15.76231172, 28.05251105, 15.56603488, 34.78641497,
20.95268019, 11.97087574, 28.16452888, 45.10068937, 32.00209717,
1.098327442, 195.4523585, 94.0545153, 20.3648651, 19.08090108,
20.26723856, 35.12860786, 38.00639611, 485.9158071, 6.801285888,
130.2613429, 26.41691724, 21.47363409, 75.24255785, 9.088017875,
17.83869051, 106.4365614, 367.7372615, 26.95847112, 42.01753212,
17.56582294, 72.00256098, 382.5705508, 150.0004825, 452.8679126,
61.51137016), Sulfide = c(5.19, 0, 72.82, 19.49, 2.93, 0, 43.95,
1.37, 23.27, 12.19, 35.69, 77.05, 4.03, 65.29, 55.12, 29.95,
14.93, 15.16, 47.67, 30.23, 75.05, 10.51, 38.75, 21.64, 35.97,
122.53, 6.95, 58.52, 75.92, 92.23, 10.85, 72.1, 28.46, 81.19,
195.59, 42.54, 277.4, 81.67), PCB = c(5.76, 1.44, 8.84, 11.92,
3.4, 17.08, 0.56, 10.56, 5.24, 1.96, 6.44, 9.44, 10.28, 12.92,
14.52, 0, 7.84, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0), PAH = c(23.36922085, 24.88374369, 21.49366333,
25.69248678, 27.47334181, 36.56726931, 478.4803895, 39.12822287,
17.2462056, 29.30102312, 232.0038657, 98.88904227, 22.6525315,
31.41940388, 29.73926409, 36.20400715, 28.34097634, 0.0479, 0.0638,
0.1312, 0.1293, 0.0589, 0.1032, 0.2725, 0.0712, 0.1173, 0.0703,
0.2097, 0.1261, 0.0685, 0.0796, 0.1353, 0.0354, 0.0323, 0.034,
0.0269, 0.0952, 0.0269), OCP = c(0.165265157, 0.004517346, 0.417073616,
2.155375191, 0, 23.48084273, 0, 2.096700845, 1.852219063, 0.074522052,
0.694281604, 0.112198511, 0.171174141, 4.644606351, 0.969985822,
1.942156359, 2.36619641, 0.01071845, 0, 0, 0, 0, 0.004247812,
0, 0, 0, 0.002020821, 0, 0.055799207, 0.003690873, 0.019063717,
0, 0.173323781, 0.010429405, 0, 0, 0.013486877, 0)), class = "data.frame", row.names = c(NA,
-38L))
