169 lines
6.8 KiB
R
169 lines
6.8 KiB
R
# tocID <- "BIN-PHYLO-Tree_building.R"
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#
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# Purpose: A Bioinformatics Course:
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# R code accompanying the BIN-PHYLO-Tree_building unit.
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#
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# Version: 1.2
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#
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# Date: 2017-10 2020-09
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# Author: Boris Steipe (boris.steipe@utoronto.ca)
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#
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# Versions:
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# 1.2 deprecate save()/load() for saveRDS()/readRDS(); Mac:
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# instructions to authorize proml.app
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# 1.1 Change from require() to requireNamespace(),
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# use <package>::<function>() idiom throughout,
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# 1.0 First 2017 version
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# 0.1 First code copied from 2016 material.
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#
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#
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# TODO:
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# Add MrBayes
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# https://cran.r-project.org/web/packages/phangorn/vignettes/IntertwiningTreesAndNetworks.html
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#
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# == DO NOT SIMPLY source() THIS FILE! =======================================
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#
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# If there are portions you don't understand, use R's help system, Google for an
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# answer, or ask your instructor. Don't continue if you don't understand what's
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# going on. That's not how it works ...
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#
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# ==============================================================================
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#TOC> ==========================================================================
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#TOC>
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#TOC> Section Title Line
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#TOC> -----------------------------------------------------------
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#TOC> 1 Calculating Trees 48
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#TOC> 1.1 PROMLPATH ... 68
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#TOC> 1.1.1 ... on the Mac 73
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#TOC> 1.1.2 ... on Windows 101
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#TOC> 1.1.3 ... on Linux 115
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#TOC> 1.1.4 Confirming PROMLPATH 120
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#TOC> 1.2 Building a maximum likelihood tree 134
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#TOC>
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#TOC> ==========================================================================
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# = 1 Calculating Trees ===================================================
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# Follow the instructions found at phylip's home on the Web to install. If you
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# are on a Windows computer, take note of the installation directory.
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# After you have installed Phylip on your computer, install the R package that
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# provides an interface to the Phylip functions.
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if (! requireNamespace("Rphylip", quietly = TRUE)) {
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install.packages("Rphylip")
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}
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# Package information:
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# library(help = Rphylip) # basic information
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# browseVignettes("Rphylip") # available vignettes
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# data(package = "Rphylip") # available datasets
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# This will install RPhylip, as well as its dependency, the package "ape".
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# == 1.1 PROMLPATH ... =====================================================
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# The next part may be tricky. You will need to figure out where
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# on your computer Phylip has been installed and define the path
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# to the proml program that calculates a maximum-likelihood tree.
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# === 1.1.1 ... on the Mac
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# On the Mac, the standard installation places a phylip folder
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# in the /Applications directory. That folder contains all the
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# individual phylip programs as <name>.app files. These are not
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# the actual executables, but "app" files are actually directories
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# that contain the required resources for a program to run.
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# The executable is in a subdirectory and you can point Rphylip
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# directly to that subdirectory to find the program it needs:
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# PROMLPATH <- "/Applications/phylip-3.695/exe/proml.app/Contents/MacOS"
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# However, RPHYLIP will not be able to run PHYLIP applications immediately,
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# because they have not been "signed" by the PHYLIP developers. The process
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# will terminate by your system, with a warning.
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# - Navigate to the phylip folder in your ~/Applications directory
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# - Descend into the "exe" folder and find proml.app
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# - Ctrl-click proml.app and choose "Open". A dialogue will show that
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# says: "macOS cannot verify the developer of “proml.app”.
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# Are you sure you want to open it?"
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# - Click open to continue. You may need to allow access to the terminal
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# as well. When the proml terminal session open, you can type
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# Ctrl-c to abort the program and close the window.
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#
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# This adds proml.app to the list of known-good programs and you will not
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# need to repeat this process.
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#
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# === 1.1.2 ... on Windows
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# On Windows you need to know where the programs have been installed, and you
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# need to specify a path that is correct for the Windows OS. Find the folder
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# that is named "exe", and right-click to inspect its properties. The path
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# should be listed among them.
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# If the path looks like "C:\Users\Meng\Programs\phylip-3.695\exe", then your
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# assignment has to be
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# PROMLPATH <- "C:/Users/Meng/Programs/phylip-3.695/exe"
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# (Note: "/", not "\")
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# I have heard that your path must not contain spaces, and it is prudent to
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# avoid other special characters as well.
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# === 1.1.3 ... on Linux
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# If you are running Linux I trust you know what to do. It's probably
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# something like
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# PROMLPATH <- "/usr/local/phylip-3.695/bin"
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# === 1.1.4 Confirming PROMLPATH
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# Confirm that the settings are right.
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PROMLPATH # returns the path
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list.dirs(PROMLPATH) # returns the directories in that path
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list.files(PROMLPATH) # lists the files [1] "proml" "proml.command"
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# If "proml" is NOT among the files that the last command returns, you
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# can't continue. Ask on the mailing list for advice.
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# If everything is good, you can add the line that defines PROMLPATH to
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# myScripts/.myProfile.R - the path will then be automatically set when
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# you quit RStudio and return.
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# == 1.2 Building a maximum likelihood tree ================================
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# Now read the mfa file you have saved in the BIB-PHYLO-Data_preparation unit,
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# as a "proseq" object with the read.protein() function of the RPhylip package:
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apsIn <- Rphylip::read.protein("data/APSESphyloSet.mfa")
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str(apsIn)
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# ... and you are ready to build a tree.
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# There are many fast options in PHYLIP - we will use the most _accurate_ one
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# that it has: proml, a maximum-likelihood tree building program for protein
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# data.
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# Building maximum-likelihood trees can eat as much computer time
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# as you can throw at it. Calculating a tree of 48 APSES domains
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# with default parameters of Rproml() runs for more than half a day
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# on my computer. But we have only twelve sequences here, so the
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# process will take us about 5 to 15 minutes. Run this, and anjoy a good cup
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# of coffee while you are waiting.
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apsTree <- Rphylip::Rproml(apsIn, path=PROMLPATH)
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# A quick first look:
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plot(apsTree)
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# save your tree:
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saveRDS(apsTree, file = "data/APSEStreeRproml.rds")
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# If this did not work, ask for advice.
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# [END]
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