showPairs

[Gon1976]

Hi, I want to perform parallel coordinates and clusters plot. I have 4 conditions against control and I want to observe all conditions. I try retFF <- plotClusters(data_st, data_metrics, threshVar="PValue", threshVal = 0.05, nC = 4, lineSize = 0.5, verbose = TRUE, clusterAllData = FALSE, showPairs = FALSE, vxAxis = TRUE)

but showPairs i not used (I show help on plotClusters and showPairs is not an option). So, how can I visualize all conditions and replicates of cluster DEG genes of a pair? thanks Gonzalo

[lindsayrutter]

Hi Gonzalo:

Yes, I can try to help troubleshoot this issue. Can you kindly share the output you get when you run: str(data_st) and str(data_metrics). And, can you let me know what output you get when you run:

retFF <- plotClusters(data_st, data_metrics, threshVar="PValue",
threshVal = 0.05, nC = 4, lineSize = 0.5, verbose = TRUE, clusterAllData = FALSE,
showPairs = FALSE, vxAxis = TRUE)

grid.draw(retFF[[1]])
grid.draw(retFF[[2]])
grid.draw(retFF[[3]])
grid.draw(retFF[[4]])

The showPairs parameters should have information when ??plotClusters is run. (For me, it does). But you can also find the details here.

You could always try running with showPairs = TRUE and showPairs = FALSE to see the difference it makes.

Thanks!