[R] Problems when trying to visualize clusters

[Paul Bernal]

Dear friends,

Hope you are all doing great. I am currently working with R version 4.3.1.

There are two things I wanted to accomplish:
1. Determine the optimal number of clusters for my dataset, which contains
11 market segments and two features, namely, toll revenue (aka tolls) and
number of transits (aka transits), and
2. Use a clustering algorithm and then plot the resulting cluster

I am working with the following packages:
install.packages("clustMixType")
install.packages("factoextra")
install.packages("NbClust")

This is my R code:
#Reading Required Datasets
df = as.data.frame(read_excel("dataforclustering.xlsx"))
df2 = df[,-1]
head(df2)
scaled_df = scale(df2)

#This part was to determine the optimal number of clusters
# Elbow method
fviz_nbclust(scaled_df, kmeans, method = "wss") +
  geom_vline(xintercept = 4, linetype = 2)+
  labs(subtitle = "Elbow method")

# Silhouette method
fviz_nbclust(scaled_df, kmeans, method = "silhouette")+
  labs(subtitle = "Silhouette method")

# Gap statistic
# nboot = 50 to keep the function speedy.
# recommended value: nboot= 500 for your analysis.
# Use verbose = FALSE to hide computing progression.
set.seed(123)
fviz_nbclust(scaled_df, kmeans, nstart = 25,  method = "gap_stat", nboot =
50)+
  labs(subtitle = "Gap statistic method")

Based on the elbow method, which suggested k = 4, I then used the following
code to produce the clusters and try to plot them:

df$MarketSegment <- as.factor(df$MarketSegment)

#kproto comes from the  clustMixType package
kclustalgo = kproto(df,4)
summary(kclustalgo)
plot(kclustalgo, vars = c("tolls","transits"))

The problem is that, when using the plot function, it does not generate
anything, it does not plot anything.

Below my dataset:
structure(list(MarketSegment = structure(c(12L, 8L, 4L, 5L, 8L,
8L, 9L, 2L, 8L, 11L, 11L, 12L, 5L, 4L, 10L, 10L, 9L, 11L, 5L,
10L, 10L, 9L, 9L, 9L, 4L, 11L, 10L, 9L, 11L, 4L, 7L, 1L, 2L,
7L, 4L, 6L, 4L, 5L, 4L, 6L, 5L, 11L, 10L, 9L, 8L, 11L, 2L, 4L,
5L, 12L, 10L, 5L, 4L, 5L, 10L, 10L, 11L, 2L, 12L, 5L, 10L, 8L,
8L, 2L, 8L, 13L, 6L, 7L, 4L, 10L, 8L, 3L, 5L, 2L, 7L, 13L, 5L,
5L, 2L, 12L, 4L, 5L, 5L, 12L, 10L, 5L, 11L, 9L, 4L, 2L, 4L, 2L,
9L, 5L, 11L, 10L, 4L, 11L, 12L, 9L, 11L, 10L, 4L, 13L, 4L, 2L,
4L, 5L, 6L, 13L, 2L, 5L, 10L, 3L, 13L, 8L, 11L, 9L, 8L, 10L,
4L, 2L, 11L, 2L, 9L, 4L, 12L, 10L, 8L, 12L, 8L, 10L, 11L, 2L,
8L, 4L, 12L, 9L, 8L, 8L, 11L, 11L, 2L, 9L, 10L, 8L, 12L, 2L,
11L, 8L, 11L, 4L, 2L, 3L, 3L, 8L, 13L, 5L, 5L, 6L, 6L, 2L, 9L,
10L, 2L, 7L, 6L, 2L, 1L, 7L, 6L, 13L, 1L, 2L, 4L, 5L, 12L, 9L,
11L, 9L, 8L, 2L, 9L, 9L, 5L, 11L, 2L, 12L, 2L, 8L, 12L, 4L, 5L,
4L, 10L, 2L, 9L, 2L, 2L, 2L, 9L, 11L, 2L, 12L, 2L, 10L, 12L,
9L, 4L, 12L, 10L, 5L, 12L, 1L, 6L, 5L, 8L, 10L, 9L, 10L, 4L,
7L, 8L, 1L, 9L, 3L, 3L, 1L, 4L, 4L, 2L, 4L, 10L, 11L, 8L, 2L,
9L, 2L, 5L, 4L, 12L, 4L, 5L, 4L, 9L, 4L, 4L, 12L, 9L, 2L, 8L,
12L, 4L, 3L, 7L, 3L, 10L, 7L, 8L, 2L, 6L, 1L, 3L, 6L, 13L, 7L,
13L, 9L, 13L, 8L, 3L, 10L, 10L, 5L, 12L, 9L, 8L, 8L, 11L, 10L,
8L, 12L, 8L, 5L, 9L, 4L, 12L, 11L, 4L, 8L, 5L, 10L, 11L, 11L,
2L, 12L, 5L, 10L, 9L, 13L, 1L, 7L, 9L, 9L, 10L, 3L, 2L, 1L, 8L,
8L, 9L, 10L, 2L, 8L, 13L, 6L, 12L, 4L, 8L, 10L, 9L, 10L, 10L,
5L, 11L, 8L, 8L, 4L, 12L, 8L, 12L, 10L, 9L, 12L, 5L, 11L, 2L,
5L, 5L, 10L, 5L, 5L, 9L, 9L, 5L, 2L, 9L, 1L, 8L, 13L, 7L, 3L,
5L, 1L, 1L, 9L, 10L, 7L, 5L, 3L, 1L, 4L), levels = c("Chemical Tankers",
"Container", "Crude/Product Tankers", "Dry Bulk", "General Cargo",
"LNG Carrier", "LPG Carrier", "Others", "Passengers", "Refrigerated",
"Tankers", "Vehicle Carriers", "Vehicle Carriers/RoRo"), class = "factor"),
    Toll = c(45622373.27, 30399013.74, 176306593.66, 18971118.38,
    25835490.96, 23740969.7, 22570777.11, 144378273.06, 59115267.47,
    71971071.4, 94431934.17, 14252216.8, 25040195.72, 92607705.13,
    17595512.81, 22275409.83, 6291531.04, 51104161.27, 25181172.84,
    34816907.8, 32777647.65, 7099598.51, 27689930.37, 42046359.26,
    173706597.74, 143220682.62, 59053229.17, 39369534.57, 157970209.29,
    411908086.08, 30644932.62, 141530616.2, 1086950201, 222938133.49,
    347883155.9, 160051827.89, 376203394.59, 44232336.52, 410395911.78,
    218235220.1, 35274869.37, 73258945.88, 37821693.14, 81193.19,
    25461445.17, 61671172.38, 64984959.44, 166826321.18, 21076499.39,
    88337589.73, 46904254.95, 20029152.87, 143083949.3, 21959696.81,
    52382607.59, 3478831.59, 46284549.62, 48579258.24, 47417137.43,
    25768369.63, 52765742.89, 60329234.95, 52200921.5, 911170775.2,
    27854758.26, 188077540.25, 170069.18, 46979713.12, 324994117.34,
    42136353.11, 12495006.27, 93066248.53, 46588988.04, 1203041643,
    275586213.06, 224722357.56, 38114431.53, 24457874.42, 224106,
    52935575.5, 145149052.16, 24254689.17, 21355540.17, 77826892.53,
    37047616.49, 25895846.03, 81595647.93, 18824145.98, 157687486.69,
    252355857.97, 23554769.2, 42803289.58, 6970409.95, 25223571.18,
    44521560.29, 23846694.1, 123861794, 62133036.93, 49025354.84,
    27761074.11, 93221253.37, 67681581.53, 326040777.37, 0, 353324758.38,
    914308534.52, 375236325.91, 42896733.54, 18760255.6, 198508135.47,
    1367150804.75, 42296364.22, 32848434.94, 84984870.35, 209972507.43,
    131115.79, 636385.07, 15683638.27, 27432524.55, 34767287.97,
    174026078.65, 91872590.71, 77273064.3, 115418664.65, 24248775.39,
    184598288.14, 55702797.23, 35938942.48, 37876793.27, 67595978.53,
    37585563.97, 38058681.79, 70479369.62, 181080995.57, 43367438.62,
    152817300.67, 99222096.54, 29739623.79, 7027238.12, 25482814.45,
    52706796.25, 44227271.88, 49125255.46, 7273684.04, 31550474.77,
    45171138.63, 113147627.59, 736129089, 118847881.44, 48827559.85,
    175552816, 231472438.57, 972466186.8, 20939505.12, 74784961.28,
    22048526.85, 184182792.62, 50043224.13, 46567864.3, 64096942.63,
    133561525.43, 1184603445, 27481529.81, 35823758.59, 1241926985.25,
    336005108, 175196241.59, 1417836913.5, 219080343.22, 447793583.34,
    142244858.6, 211282556.89, 282402337.27, 73904457.86, 213236.53,
    23845925.9, 47069774.11, 17091622.26, 77288315.4, 20367261.33,
    58398395.39, 230933373.58, 26598884.35, 2406557.1, 6480102,
    13628284.31, 10263514.77, 66291278.83, 45203889.46, 24439458.61,
    62995994.42, 103545550.11, 23582006.69, 106841255.81, 30920698.81,
    57152783.67, 6788655.31, 58688264.46, 63623458.42, 381280927.57,
    26160209.37, 94398586.99, 548546815.6, 94377076.67, 660333530.6,
    58467965.42, 121250943.68, 39897634.25, 253784215.75, 123264396,
    58788870.55, 41450428.73, 116407322.67, 37073625.53, 80949.5,
    46479259.97, 17935104.29, 44743486.45, 50354870.76, 45978813.8,
    381104737.29, 144588856.56, 13453753.84, 215589051.87, 14640417.36,
    113367165.56, 100614565.26, 270041980.52, 436045596.44, 399693615.37,
    80310709.08, 178202292.6, 37426161.19, 84501310.47, 35095993.84,
    115887420.17, 25320445.08, 131720569.81, 20152178.46, 98738563.37,
    52761092.05, 126078172.3, 24618706.25, 136326542.07, 11518860.78,
    156025722.98, 170794953.78, 105383146.32, 33742975.52, 786732496.2,
    44558463.25, 138272099.98, 332758968.08, 73351527.91, 3711095.76,
    0, 49843621.55, 22795131.65, 23624194.51, 960690603.6, 0,
    174697284.22, 75560763.05, 231180, 196673683.99, 190737686.99,
    213184850.38, 43204339.22, 175208475.3, 14294438.32, 105373950.72,
    34354378.94, 36201953.3, 152644.76, 4271.52, 21467521.11,
    24714178.25, 23397907.04, 84318567.96, 41391735.09, 59207931.58,
    96631125.37, 26119366.87, 24050681.28, 6414468.87, 115073972.91,
    48806783.58, 53117026.48, 143925878.71, 54427083.34, 29621363.6,
    67914181.91, 208255468.52, 172563091.58, 783130968, 87885643.22,
    33623583.6, 49862226.49, 39581084.06, 47338366.37, 0, 0,
    42059174.7, 55196029.54, 45573526.31, 77542558.18, 948435917.2,
    184766344.51, 11715869.41, 11465772.13, 58348554.79, 34159529.23,
    1324615521.7, 14214065.75, 204448377.38, 133199367.48, 48301726.87,
    171342164.62, 27932981.26, 204453.32, 13799161.85, 36545009.39,
    40127237.59, 24856336.87, 81983152.36, 27475201.4, 40720204.5,
    143732024.58, 81736659.41, 54145665.75, 63195468.9, 17990069.83,
    7063003.98, 53943424.6, 27336061.94, 49141786, 56875952.23,
    25301093.8, 21993181.36, 52955818.55, 25793889.09, 28102485.94,
    39856771.5, 45181483.95, 42949296.26, 931539910.4, 34918600.8,
    134194366.11, 20115045.15, 203545729.19, 68836834.76, 85618322.31,
    41411914.83, 203629971.2, 200898608.18, 44469248.2, 35518487.49,
    326654852.92, 38518260.2, 99286360.37, 231011004.03, 368789029.42
    ), Transits = c(557, 2932, 3312, 1015, 3037, 2958, 257, 1797,
    2812, 1615, 1912, 251, 1836, 2861, 1592, 1908, 149, 1656,
    1596, 2613, 2409, 159, 205, 235, 2472, 2079, 1631, 202, 1838,
    3356, 298, 1489, 2493, 1148, 2614, 421, 2758, 651, 2925,
    519, 453, 2187, 2568, 2799, 2705, 1928, 1187, 3042, 968,
    789, 2216, 817, 2380, 882, 2371, 324, 1667, 1120, 646, 819,
    2108, 2737, 2586, 3255, 2210, 796, 4, 440, 2610, 838, 1217,
    667, 675, 2615, 1349, 886, 556, 1514, 37622, 665, 3431, 1537,
    1075, 721, 1997, 1333, 2081, 217, 2579, 2534, 703, 992, 226,
    1771, 1591, 1963, 3306, 1943, 611, 224, 1707, 2151, 3288,
    2510, 3081, 2892, 3075, 678, 58, 798, 2642, 616, 566, 413,
    691, 22076, 9415, 300, 2881, 2309, 3613, 1428, 1940, 1691,
    310, 3549, 561, 2021, 3071, 645, 2641, 2085, 1704, 2126,
    2668, 2851, 792, 243, 682, 2881, 1810, 1615, 1043, 170, 2140,
    2615, 833, 3524, 2027, 2497, 2342, 2982, 3326, 181, 596,
    1986, 787, 878, 813, 181, 340, 2616, 127, 746, 2537, 1526,
    425, 2843, 1987, 1552, 343, 782, 1850, 1334, 8088, 1431,
    509, 283, 2216, 228, 2625, 2451, 225, 75, 485, 472, 237,
    1091, 1069, 2785, 973, 3092, 1597, 3134, 2279, 1093, 155,
    1131, 1174, 3020, 221, 1744, 3419, 728, 3604, 2199, 765,
    215, 3033, 632, 1453, 926, 504, 431, 2, 913, 2001, 992, 265,
    954, 2904, 929, 1696, 2114, 53, 783, 628, 2362, 3004, 2781,
    1391, 3939, 2031, 2207, 2653, 1597, 299, 1749, 1061, 3019,
    731, 3206, 1558, 3275, 233, 2598, 2752, 810, 248, 3235, 2455,
    618, 3220, 647, 51, 3611, 1069, 240, 2086, 3132, 2975, 1799,
    610, 3, 802, 1027, 844, 170, 650, 1314, 631, 601, 459, 8494,
    1803, 297, 2909, 2941, 2129, 2172, 2643, 807, 2893, 1767,
    214, 3109, 676, 1804, 2346, 2692, 856, 1912, 2404, 2264,
    3094, 448, 900, 1088, 214, 202, 4921, 3567, 229, 249, 968,
    621, 2824, 1886, 1989, 2034, 265, 590, 2425, 1521, 762, 272,
    600, 3928, 2811, 5552, 308, 2474, 2442, 1379, 2280, 2897,
    2794, 2611, 761, 2795, 1110, 1623, 209, 810, 1681, 1642,
    1092, 1677, 825, 2246, 779, 816, 226, 214, 908, 3010, 204,
    1503, 1944, 849, 538, 666, 636, 2019, 1994, 196, 665, 1552,
    559, 569, 2048, 2170)), row.names = c(NA, -362L), class = "data.frame")

Any guidance will be greatly appreciated.

Best regards,
Paul

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