Dear all.
I am trying to output an MDS plot to understand the relationship between RNAseq data.
I was able to output the MDS plot using “diffExpr.P0.001_C2.matrix” output by edgeR. However, I would like to use ggplot2 to output it in a more readable form.
I have tried the following steps, but I am getting an error.
What is the problem with my pipeline?
Thank you very much for your advices!
> d <- dist(1 - rho)
> d
Control1 Control2 Dry1 Dry2 DryRec1 DryRec2 PreRec1 PreRec2 Predry1
Control2 0.06502264
Dry1 1.48474438 1.52669729
Dry2 1.62197906 1.66162549 0.22807033
DryRec1 1.63688521 1.67153910 0.45567746 0.34034233
DryRec2 1.54150125 1.57960816 0.30996896 0.28957991 0.23296231
PreRec1 1.60822608 1.64742160 0.24699751 0.15173269 0.34458096 0.28891000
PreRec2 1.63382533 1.67045446 0.35367499 0.20514152 0.28429467 0.32059748 0.18160279
Predry1 1.54096592 1.58217537 0.15757815 0.19393518 0.42187210 0.29722224 0.18873484 0.30663769
Predry2 1.63482837 1.67433055 0.25604187 0.11518698 0.33440870 0.29088779 0.13758830 0.19564874 0.18327134
> mds <- cmdscale(d)
> plot(mds, type = "n")
> text(mds, labels = colnames(count))
> mds2 <- as.data.frame(as.matrix(mds))
> ggplot(mds2, aes(x = `1`, y = `2`, color = dex, shape = cell))
Error in FUN(X[[i]], ...) : object '1' not found
> dput(mds2)
structure(list(V1 = c(-1.25870472974072, -1.29753868680971, 0.214130257699255,
0.359880006140221, 0.354475784656956, 0.269322460991461, 0.34548218958249,
0.366016370053708, 0.273662948738074, 0.373273398688271), V2 = c(-0.00570676794533206,
0.0186976427031538, -0.153998283521261, -0.060516886861918, 0.266222331907919,
0.126701199467327, -0.0536343596445791, 0.0529305521126579, -0.13730725971642,
-0.0533881685015465)), class = "data.frame", row.names = c("Control1",
"Control2", "Dry1", "Dry2", "DryRec1", "DryRec2", "PreRec1",
"PreRec2", "Predry1", "Predry2"))
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