我想对我的数据进行聚类分析：
library(cluster)
library(ade4)
data=read.table("L5.txt",header=T,row.names=1,dec=".",sep="\t")
JSD <- function(x,y) sqrt(0.5 * KLD(x, (x+y)/2) + 0.5 * KLD(y, (x+y)/2))
KLD <- function(x,y) sum(x * log(x/y))
dist.JSD <- function(inMatrix, pseudocount=0.000001, ...) {
KLD <- function(x,y) sum(x *log(x/y))
JSD<- function(x,y) sqrt(0.5 * KLD(x, (x+y)/2) + 0.5 * KLD(y, (x+y)/2))
matrixColSize <- length(colnames(inMatrix))
matrixRowSize <- length(rownames(inMatrix))
colnames <- colnames(inMatrix)
resultsMatrix <- matrix(0, matrixColSize, matrixColSize)
inMatrix = apply(inMatrix,1:2,function(x) ifelse (x==0,pseudocount,x))
for(i in 1:matrixColSize) {
for(j in 1:matrixColSize) {
resultsMatrix[i,j]=JSD(as.vector(inMatrix[,i]),
as.vector(inMatrix[,j]))
}
}
colnames -> colnames(resultsMatrix) -> rownames(resultsMatrix)
as.dist(resultsMatrix)->resultsMatrix
attr(resultsMatrix, "method") <- "dist"
return(resultsMatrix)
}
data.dist=dist.JSD(data)
pam.clustering=function(x,k) { # x is a distance matrix and k the number of clusters
require(cluster)
cluster = as.vector(pam(as.dist(x), k, diss=TRUE)$clustering)
return(cluster)
}
我发现我的数据的最佳簇数是2，所以我做了：
data.cluster=pam.clustering(data.dist,k=2)
obs.pca=dudi.pca(data.frame(t(data)), scannf=F, nf=10)
obs.bet=bca(obs.pca, fac=as.factor(data.cluster), scannf=F, nf=k-1)
但是当我尝试使用sclass绘制结果时，我收到了一个错误：
s.class(obs.bet$ls, fac=as.factor(data.cluster), grid=F)
Errore in `[.data.frame`(dfxy, , yax) : undefined columns selected
相反，如果我使用k = 3，它就有效......
有谁知道问题出在哪里？
我的数据如下：
structure(list(X12.BA.V = c(0, 0, 0.33506013, 0, 0, 0.032747456,
0.06919519, 0.119148936, 0.010545791, 0.024051804, 0.001480111,
0.000370028, 0.000555042, 0.023311748, 0.008510638, 0.000740056,
0.018871415, 0.000185014, 0, 0.175763182, 0.000370028, 0.02146161,
0, 0, 0.007955597, 0, 0, 0, 0), X37.TO.O = c(0.000718219, 0.066076131,
0.391429255, 0, 0.000239406, 0.001197031, 0.024658846, 0.015800814,
0.002394063, 0.005266938, 0, 0, 0.000478813, 0.000239406, 0.036868566,
0, 0.068470194, 0.001197031, 0.000478813, 0.001675844, 0.004788125,
0.002394063, 0.000239406, 0, 0.016519033, 0, 0, 0.005027532,
0), X29.TO.VG = c(0.0004004, 0.008808809, 0.181581582, 0.017817818,
0.036036036, 0.025425425, 0.05985986, 0.052252252, 0.011211211,
0.038038038, 0.003603604, 0, 0.037037037, 0.084684685, 0.009009009,
0.005405405, 0.057057057, 0.0004004, 0, 0.18018018, 0.003403403,
0.032432432, 0, 0, 0.017417417, 0, 0, 0, 0), X04.BA.V = c(0,
0.001625135, 0.084507042, 0.000812568, 0.018418202, 0.023564464,
0.06744312, 0.127843987, 0.005417118, 0.10780065, 0.000812568,
0, 0.023293608, 0.02383532, 0.00595883, 0.003521127, 0.086403034,
0.000270856, 0.000812568, 0.111863489, 0.004062839, 0.066901408,
0, 0, 0.020855905, 0, 0, 0, 0), X31.TO.O = c(0.000243309, 0.03406326,
0.16836983, 0, 0, 0.04379562, 0.105109489, 0.198296837, 0.032360097,
0.020681265, 0.008759124, 0, 0.000243309, 0.018978102, 0.021167883,
0.000729927, 0.01946472, 0.000243309, 0.000973236, 0.191240876,
0.006812652, 0, 0, 0, 0, 0, 0, 0.00243309, 0), X01.BA.V = c(0.001183992,
0.010419133, 0.058962823, 0.007340753, 0.320625148, 0.008524745,
0.062988397, 0.072933933, 0.010419133, 0.092825006, 0, 0, 0.007340753,
0.014681506, 0.008761544, 0.001183992, 0.041676533, 0, 0, 0.041676533,
0.002131186, 0.016812692, 0, 0, 0.063698792, 0, 0, 0, 0), X01.TO.VG = c(0,
0.000596125, 0.250074516, 0, 0, 0.015499255, 0.039940387, 0.015797317,
0.001788376, 0.030104322, 0, 0, 0.037555887, 0.030700447, 0.00119225,
0.003874814, 0.030700447, 0, 0.005067064, 0.093591654, 0.010730253,
0.246199702, 0, 0, 0.007153502, 0, 0, 0.001788376, 0), X19.BO.VG = c(0,
0.017184785, 0.002896312, 0, 0.343309519, 0.009654373, 0.033790307,
0.034562657, 0.005213362, 0.019694922, 0.00077235, 0.000579262,
0.001737787, 0.007530411, 0.009847461, 0.001930875, 0.087854798,
0, 0.000579262, 0.067966789, 0.049623479, 0.01602626, 0, 0, 0.001351612,
0, 0.0015447, 0, 0.000193087), X32.BO.VG = c(0, 0.004503437,
0.219720313, 0, 0, 0.031050012, 0.061863001, 0.105001185, 0.006399621,
0.028205736, 0.000711069, 0.001185115, 0.029153828, 0.059492771,
0.005925575, 0.003318322, 0.050485897, 0, 0.00237023, 0.118748519,
0.00474046, 0.039819863, 0, 0, 0, 0, 0, 0.004029391, 0.000237023
), X27.TO.V = c(0.00033428, 0.020892529, 0.397793749, 0.00701989,
0, 0.006852749, 0.015544041, 0.021226809, 0.002172823, 0.009861274,
0.001169982, 0, 0.004178506, 0.052816313, 0.001002841, 0.000501421,
0.055824837, 0.00033428, 0.011031255, 0.047634966, 0.00718703,
0.026408156, 0, 0, 0.001002841, 0, 0, 0.00016714, 0), X24.TO.V = c(0,
0.140040241, 0.151911469, 0.006841046, 0, 0.007243461, 0.053521127,
0.01167002, 0.003420523, 0.037826962, 0.000603622, 0.000201207,
0.006841046, 0.015694165, 0.003822938, 0.003219316, 0.06861167,
0.000603622, 0.004024145, 0.041448692, 0.010663984, 0.029376258,
0, 0, 0.001810865, 0, 0, 0, 0), X26.TO.VG = c(0.000502428, 0.058951599,
0.173840228, 0, 0.0294758, 0.004186903, 0.008876235, 0.008206331,
0.001507285, 0.015910233, 0.000502428, 0.000167476, 0.00301457,
0.002344666, 0.003349523, 0.004689332, 0.094289064, 0.001674761,
0.038184559, 0.030983085, 0.049572936, 0.019762184, 0.000502428,
0, 0, 0, 0, 0, 0), X06.BO.O = c(0.000533476, 0.001066951, 0.113630301,
0, 0.000266738, 0.029607895, 0.044278474, 0.12590024, 0.005601494,
0.035742865, 0.004001067, 0, 0, 0.144305148, 0.022939451, 0.002934116,
0.093091491, 0.000266738, 0, 0.155241398, 0.002133902, 0.038943718,
0.001333689, 0, 0.025873566, 0, 0, 0, 0.012803414), X15.BO.VG = c(0,
0, 0.327540107, 0, 0.000891266, 0.012477718, 0.076871658, 0.169340463,
0.005347594, 0.071301248, 0.000222816, 0, 0.000222816, 0.00802139,
0.014483066, 0.000222816, 0.009581105, 0.000668449, 0, 0.084224599,
0.001336898, 0.000445633, 0, 0, 0.028743316, 0, 0, 0.007575758,
0)), .Names = c("X12.BA.V",
"X37.TO.O", "X29.TO.VG", "X04.BA.V", "X31.TO.O", "X01.BA.V",
"X01.TO.VG", "X19.BO.VG", "X32.BO.VG", "X27.TO.V", "X24.TO.V",
"X26.TO.VG", "X06.BO.O", "X15.BO.VG", "X25.BO.VG"), class = "data.frame", row.names = c("Bacteroidia;Other;Other",
"Bacteroidia;f__;g__", "Bacteroidaceae;g__Bacteroides", "Prevotellaceae;g__",
"Prevotellaceae;g__Prevotella", "Lachnospiraceae;Other", "Lachnospiraceae;g__",
"Lachnospiraceae;g__Blautia", "Lachnospiraceae;g__Clostridium",
"Lachnospiraceae;g__Coprococcus", "Lachnospiraceae;g__Eubacterium",
"Lachnospiraceae;g__Lachnobacterium", "Lachnospiraceae;g__Lachnospira",
"Lachnospiraceae;g__Roseburia", "Lachnospiraceae;g__Ruminococcus",
"Ruminococcaceae;Other", "Ruminococcaceae;g__", "Ruminococcaceae;g__Clostridium",
"Ruminococcaceae;g__Eubacterium", "Ruminococcaceae;g__Faecalibacterium",
"Ruminococcaceae;g__Oscillospira", "Ruminococcaceae;g__Ruminococcus",
"Veillonellaceae;g__", "Veillonellaceae;g__Acidaminococcus",
"Veillonellaceae;g__Dialister", "Veillonellaceae;g__Megamonas",
"Veillonellaceae;g__Megasphaera", "Veillonellaceae;g__Phascolarctobacterium",
"Veillonellaceae;g__Veillonella"))