Cannot plot clusters

[HCY558]

Hello,
I was wondering if you can help me with the following error? Thank you!

I am using the BigPint pipeline on my own RNAseq data. Everything works up until this point, I can create the parallel coordinate plots just fine, but then when I try to create clusters I get this error. I am using R 4.3.0 and Rstudio 2023.03.1

#set number of clusters and plot each
ret <- plotClusters(data, dataMetrics, threshVal = 0.05, nC = 4,
colList = c("#00A600FF", "#CC00FFFF"), lineSize = 0.5, verbose = TRUE)

Error in xtfrm.data.frame(x) : cannot xtfrm data frames

[lindsayrutter]

Hello:

Yes, I can try to help you solve that error.

One comment: You set nC (number of clusters) to a value of 4. However, you only provided 2 colors to your colList (color list). If your script were to work, then it would create four subplots (one for each of your 4 clusters), but only 2 of them would display colored lines (the other 2 would just be blank canvas). So, be sure to keep nC and colList equal in value. When you then draw your clustered plot (with the grid.draw function), be sure to use that same value in the naming scheme. Below are two examples:

2-cluster example:

ret <- plotClusters(data, dataMetrics, threshVal = 0.05, nC = 2, colList = c("#00A600FF", "#CC00FFFF"), lineSize = 0.5, verbose = TRUE)

grid.draw(ret[["N_P_2"]]) # value is 2

4-cluster example:

ret <- plotClusters(data, dataMetrics, threshVal = 0.05, nC = 4, colList = c("#00A600FF", "#CC00FFFF", "#0066FF", "#CC00FF"), lineSize = 0.5, verbose = TRUE)

grid.draw(ret[["N_P_4"]]) # value is 4

I am currently unsure about the error. So, to troubleshoot that, could you kindly paste what you get when you type:

str(data)
str(dataMetrics)

That might help me pinpoint the problem! Thank you!