How to plot dendogram based on samples ID
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 <nabiyogesh at 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
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