Error in hclustplot use-annotation not found

[Former user]

http://thegrantlab.org/bio3d/tutorials/principal-component-analysis

hclustplot(hc.rd, colors=annotation[, "color"], labels=pdbs$id, cex=0.5, ylab="RMSD (Å)", main="RMSD Cluster Dendrogram", fillbox=FALSE)

Error in hclustplot(hc.rd, colors = annotation[, "color"], labels = pdbs$id, : object 'annotation' not found

[Xinqiu Yao]

Hi,

This is not a bug. We strongly recommend you go through the tutorial in one single R session and execute every chunk of codes. Otherwise you may miss some data in your workspace. In this example, you probably skipped the step 'attach(transducin)', which loads necessary data for the plotting here. This step is noted in the tutorial, section "Exploring example data for the transducin heterotrimeric G Protein".

[Barry Grant]

Basically you are missing the 'annotation' object that was created in an earlier step of the tutorial. In this code snippet 'annotation' it is used as a color vector for the plot produced.

To solve this you should run the earlier step related to 'attach(transducin)' or create your own color vector and use it here in place of 'annotation'.

I will mark this as resolved but do reopen if you experience further problems.