Neither ContigID nor sampleID are defined in your example. The default
is to plot by the row names. You can get the manual page for the
dendrogram plot using the command ?plot.hclust. The second argument
lets you specify the labels.
David L Carlson, retired
Department of Anthropology
Texas A&M University
On Sat, Jun 8, 2019 at 4:48 AM Yogesh Gupta <nabiyog...@gmail.com> wrote:
>
> 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]]
>
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