[R] How to plot dendogram based on samples ID

[Yogesh Gupta]

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

	[[alternative HTML version deleted]]