How to plot dendogram based on samples ID
Hi, I do have RNAseq FPKM count and interested in dendrogram for samples cluster. I used below code but it generate dendogram based on ContigID instead of sampleID.
countMatrix = read.table("Trinity_trans.counts.matrix.txt",header=T,sep='\t',check.names=F,row.names=1)
dim(countMatrix)
[1] 142686 6
head(countMatrix)
AS_0DAP AS_4DAP AS_8DAP NMK_0DAP NMK_4DAP NMK_8DAP TRINITY_DN17944_c0_g1_i11 14.32 24.63 8.21 4.54 20 8.49 TRINITY_DN7591_c0_g1_i1 0.00 0.00 1.00 3.00 3 0.00 TRINITY_DN28918_c0_g1_i1 1.00 2.00 1.00 0.00 2 0.00 TRINITY_DN14082_c2_g2_i5 6.00 5.00 1.00 0.00 1 0.00 TRINITY_DN31994_c0_g1_i1 1.00 2.00 0.00 0.00 0 3.00 TRINITY_DN19560_c0_g1_i1 1.00 3.00 0.00 0.00 1 1.00
rv <- rowVars(countMatrix) summary(rv)
Min. 1st Qu. Median Mean 3rd Qu. Max. 0.000e+00 1.000e+00 1.500e+01 3.570e+05 5.180e+02 4.122e+09
(q75 <-quantile(rowVars(countMatrix), .75))
75% 518.3202
m2 <- countMatrix[rv >q75, ] dim(m2)
[1] 35672 6
summary(rowVars(m2))
Min. 1st Qu. Median Mean 3rd Qu. Max. 5.180e+02 1.670e+03 6.677e+03 1.428e+06 4.101e+04 4.122e+09
d <- dist(m2, method="euclidean") h <-hclust(d, method="complete") plot(h)
Kind Regards Yogesh