I have been trying to do this using the packages ape and also phyloseq in R, but have found it challenging. I have a tree that I made for each individual sequence (120 total) and I have individual inhibition scores for each isolates. I would like to group the bacteria at the genus, or maybe even family level and show this tree. Then, I want to put at the end of the tips the average inhibition score of that taxonomic group with a bar plot with error bars. Any suggestions?
Hi Carly! I don't have the APE book with me right now, but I think that what you want to do would require tree manipulation on one side (collapsing your terminal clades into tips to reflect genus/family), and calculating the average scores on the other side and plotting alongside the tips.
Each node and tip of the tree has a unique identifier (you can find where it is within the tree object by using str() to figure out the different parts or looking up the object class definition). Try extracting the vector of tip labels, and creating a parallel vector with the values you want to pair to the tips. Then you can use it to label the tips or even make plots based on those values.
Sorry for the lack of concrete code, I'll look it up tonight when I get back home.
Hi Ed! Hope all is well! Thanks for the info. I have been using phyloseq in R and making some progress today. I can use the taxa_glom function in this package and it can group taxa by different taxonomic levels and I can make a tree with it using plot_tree. Then I have made a second figure with inhibition scores using ggplot2 and am in the process of trying to pair those two figures. I think it is coming along now after a few days of struggle....I would be interested in code using ape to do this if it is easy enough for you to find to try to see if taxa_glom and using the ape package makes a similar tree. No worries if not.
Cheers,
Carly
I think you can use the function tiplabels to put your values on the tips. I know that nodelabels can put small plots on the nodes of the tree. I used it in my latest paper (Fig. 7, check it out), and maybe tiplabels can do the same. I bit the bullet and bought Emmanuel Paradis' book about Ape. It is quite useful.
http://www.frontiersinzoology.com/content/12/1/8
There is a copy in my profile here too. I could clean up the code a bit and upload it too.
I am not really good with R but have used the package ARB for similar things.
I suggest ARB as well, you can find further informations at http://www.arb-silva.de
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools