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Data X:
kk1_1_R1_R2 kk1_2_R1_R2 7kk_1_R1_R2 7kk_2_R1_R2 GG2335|c0_g1 0.000 0.000 1.047 0.313 GG1949|c10_g1 0.560 0.941 0.000 0.865 GG19775|c2_g1 0.000 0.861 0.000 0.000 GG10182|c7_g1 0.000 0.367 0.834 0.928 GG20880|c5_g1 0.704 0.000 0.232 0.000 GG18785|c0_g1 170.253 277.297 292.272 306.461 GG1852|c0_g1 115.506 101.047 108.864 82.721 GG18116|c0_g2 6.156 8.653 5.547 7.213 GG15867|c1_g2 0.415 0.597 0.167 0.365 GG18183|c0_g2 2.248 0.734 1.667 2.126 GG15403|c6_g1 3.629 0.000 6.186 4.826 GG18453|c1_g1 1.065 0.000 0.000 0.000 GG19167|c11_g1 0.000 0.000 1.130 0.000 GG15276|c1_g1 6.969 13.014 2.741 9.808 GG15205|c0_g2 7.889 9.181 8.409 9.642 GG5606|c6_g1 1.390 0.000 0.194 0.292 GG4136|c2_g1 27.324 37.125 29.339 34.887 GG1315|c0_g1 2.103 0.712 1.250 0.000 GG18466|c0_g1 1.760 0.505 0.954 0.771 GG1210|c4_g1 0.298 1.056 0.593 1.303 GG13717|c0_g1 0.370 0.000 0.000 0.552 GG12208|c1_g2 1.128 0.000 1.676 3.513 GG15480|c0_g1 470.318 544.232 513.622 599.548 GG4007|c1_g1 145.556 87.218 99.474 136.923 GG17158|c1_g1 1.507 1.687 1.343 1.584 GG14355|c1_g2 1.110 0.000 0.157 0.000 GG7780|c0_g1 0.343 0.585 0.000 0.490 GG10134|c0_g1 2.564 7.184 5.446 3.669 GG9796|c1_g1 2.049 0.000 0.000 0.208 GG16111|c0_g4 0.803 0.264 0.519 0.521 GG19236|c0_g1 239.912 378.482 258.709 370.346 GG15049|c0_g1 30.826 29.207 37.989 33.147 GG6824|c0_g1 1.128 1.400 1.482 1.564 GG16396|c1_g1 0.505 0.608 0.407 0.719 GG11748|c9_g1 1.480 0.000 1.102 0.000 GG8281|c3_g1 0.912 0.000 0.380 0.188
Names of X columns:
data
Method
complete
ward
single
complete
average
mcquitty
median
centroid
# of (top) clusters to display
ALL
ALL
2
3
4
5
6
7
8
9
10
15
20
Horizontal
TRUE
FALSE
TRUE
Triangle
TRUE
FALSE
TRUE
Chart options
Title:
Label y-axis:
Label x-axis:
R Code
par3 <- as.logical(par3) par4 <- as.logical(par4) if (par3 == 'TRUE'){ dum = xlab xlab = ylab ylab = dum } x <- t(y) hc <- hclust(dist(x),method=par1) d <- as.dendrogram(hc) str(d) mysub <- paste('Method: ',par1) bitmap(file='test1.png') if (par4 == 'TRUE'){ plot(d,main=main,ylab=ylab,xlab=xlab,horiz=par3, nodePar=list(pch = c(1,NA), cex=0.8, lab.cex = 0.8),type='t',center=T, sub=mysub) } else { plot(d,main=main,ylab=ylab,xlab=xlab,horiz=par3, nodePar=list(pch = c(1,NA), cex=0.8, lab.cex = 0.8), sub=mysub) } dev.off() if (par2 != 'ALL'){ if (par3 == 'TRUE'){ ylab = 'cluster' } else { xlab = 'cluster' } par2 <- as.numeric(par2) memb <- cutree(hc, k = par2) cent <- NULL for(k in 1:par2){ cent <- rbind(cent, colMeans(x[memb == k, , drop = FALSE])) } hc1 <- hclust(dist(cent),method=par1, members = table(memb)) de <- as.dendrogram(hc1) bitmap(file='test2.png') if (par4 == 'TRUE'){ plot(de,main=main,ylab=ylab,xlab=xlab,horiz=par3, nodePar=list(pch = c(1,NA), cex=0.8, lab.cex = 0.8),type='t',center=T, sub=mysub) } else { plot(de,main=main,ylab=ylab,xlab=xlab,horiz=par3, nodePar=list(pch = c(1,NA), cex=0.8, lab.cex = 0.8), sub=mysub) } dev.off() str(de) } load(file='createtable') a<-table.start() a<-table.row.start(a) a<-table.element(a,'Summary of Dendrogram',2,TRUE) a<-table.row.end(a) a<-table.row.start(a) a<-table.element(a,'Label',header=TRUE) a<-table.element(a,'Height',header=TRUE) a<-table.row.end(a) num <- length(x[,1])-1 for (i in 1:num) { a<-table.row.start(a) a<-table.element(a,hc$labels[i]) a<-table.element(a,hc$height[i]) a<-table.row.end(a) } a<-table.end(a) table.save(a,file='mytable1.tab') if (par2 != 'ALL'){ a<-table.start() a<-table.row.start(a) a<-table.element(a,'Summary of Cut Dendrogram',2,TRUE) a<-table.row.end(a) a<-table.row.start(a) a<-table.element(a,'Label',header=TRUE) a<-table.element(a,'Height',header=TRUE) a<-table.row.end(a) num <- par2-1 for (i in 1:num) { a<-table.row.start(a) a<-table.element(a,i) a<-table.element(a,hc1$height[i]) a<-table.row.end(a) } a<-table.end(a) table.save(a,file='mytable2.tab') }
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