ydeng/bch441-work-abc-units
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Deprecate iTol and use taxize:: instead. Rewrite of tip re-ordering.

Browse Source
This commit is contained in:
hyginn 2020-09-26 21:39:18 +10:00
parent 68b00c83e8
commit 777cabcb20
1 changed files with 121 additions and 50 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

171
BIN-PHYLO-Tree_analysis.R
View File

@ -1,20 +1,17 @@
# tocID <- "BIN-PHYLO-Tree_analysis.R"
#
# ---------------------------------------------------------------------------- #
# PATIENCE ... #
# Do not yet work wih this code. Updates in progress. Thank you. #
# boris.steipe@utoronto.ca #
# ---------------------------------------------------------------------------- #
#
# Purpose: A Bioinformatics Course:
# R code accompanying the BIN-PHYLO-Tree_analysis unit.
#
# Version: 1.1
# Version: 1.2
#
# Date: 2017 10 - 2019 01
# Date: 2017-10 - 2020-09
# Author: Boris Steipe (boris.steipe@utoronto.ca)
#
# Versions:
# 1.2 2020 updates. Deprecate iTol and use taxize:: instead.
# Rewrite of tip re-ordering. Better handling of
# messages. pBar() for randomization.
# 1.1 Change from require() to requireNamespace(),
# use <package>::<function>() idiom throughout,
# use Biocmanager:: not biocLite()
@ -37,15 +34,16 @@
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#TOC> --------------------------------------------------
#TOC> 1 Preparation and Tree Plot 46
#TOC> 2 Tree Analysis 86
#TOC> 2.1 Rooting Trees 145
#TOC> 2.2 Rotating Clades 190
#TOC> 2.3 Computing tree distances 241
#TOC>
#TOC> 1 Preparation and Tree Plot 50
#TOC> 2 SPECIES REFERENCE TREE 66
#TOC> 3 Tree Analysis 117
#TOC> 3.1 Rooting Trees 177
#TOC> 3.2 Rotating Clades 222
#TOC> 3.3 Computing tree distances 309
#TOC>
#TOC> ==========================================================================
@ -60,36 +58,63 @@ if (! requireNamespace("ape", quietly = TRUE)) {
# browseVignettes("ape") # available vignettes
# data(package = "ape") # available datasets
# We change the graphics parameters from time to time, let's define the
# default so we can recreate a sane state:
dev.off()
PAR <- par()
# Read the species tree that you have created at the phyloT Website:
fungiTree <- ape::read.tree("fungiTree.txt")
# = 2 SPECIES REFERENCE TREE ==============================================
# Before we do any kind of phylogenetic analysis of genes from several species,
# we MUST have a reference tree of the taxonomic relationships in hand. This
# context is absolutely required for the interpretation of our tree.
# We have the tax-ids in our database, and the NCBI has the species tree - we just need some way to extract the subtree that corresponds to our taxons of interest. Here's how to use the taxize:: package.
if (! requireNamespace("taxize", quietly = TRUE)) {
install.packages("taxize")
}
# Package information:
# library(help = taxize) # basic information
# browseVignettes("taxize") # available vignettes
# data(package = "taxize") # available datasets
( mySOI <- c(myDB$taxonomy$ID, "83333") )
myClass <- taxize::classification(mySOI, db = "ncbi")
str(myClass)
myClass[[1]]
fungiTree <- taxize::class2tree(myClass, check = TRUE)
plot(fungiTree)
# The tree produced by phyloT contains full length species names, but it would
# be more convenient if it had bicodes instead.
# The tree produced by taxize:: contains full length species names,
# but it would be more convenient if it had bicodes instead. Also, the actual
# tree is only part of the list(), which will cause problems later:
str(fungiTree)
# The species names are in a vector $tip.label of this list. We can use bicode()
# to shorten them - but note that they have underscores as word separators. Thus
# we will use gsub("-", " ", ...) to replace the underscores with spaces.
# we therefor simplify
fungiTree <- fungiTree$phylo
str(fungiTree)
for (i in seq_along(fungiTree$tip.label)) {
fungiTree$tip.label[i] <- biCode(gsub("_", " ", fungiTree$tip.label[i]))
}
# The species names are in a vector $phylo$tip.label of this list.
# We can use biCode() to shorten them.
fungiTree$tip.label <- biCode(fungiTree$tip.label)
# Plot the tree
plot(fungiTree, cex = 1.0, root.edge = TRUE, no.margin = TRUE)
nSP <- length(fungiTree$tip.label)
plot(fungiTree, cex = 0.8, root.edge = TRUE, no.margin = TRUE)
text(-1, nSP - 0.5, "Species Tree:\nFungi", pos = 4)
ape::nodelabels(text = fungiTree$node.label,
cex = 0.6,
adj = 0.2,
bg = "#D4F2DA")
# Note that you can use the arrow buttons in the menu above the plot to scroll
# back to plots you have created earlier - so you can reference back to the
# species tree.
# Note that you can use the arrow buttons in the menu above the plot pane to
# scroll back to plots you have created earlier - so you can reference back to
# this species tree in your later analysis.
# = 2 Tree Analysis =======================================================
# = 3 Tree Analysis =======================================================
# 1.1 Visualizing your tree
@ -110,7 +135,7 @@ ape::nodelabels(text = fungiTree$node.label,
# We load the APSES sequence tree that you produced in the
# BIN-PHYLO-Tree_building unit:
apsTree <- readRDS(file = "APSEStreeRproml.rds")
apsTree <- readRDS(file = "data/APSEStreeRproml.rds")
plot(apsTree) # default type is "phylogram"
plot(apsTree, type = "unrooted")
@ -144,11 +169,12 @@ ape::Nnode(apsTree)
ape::Nedge(apsTree)
ape::Ntip(apsTree)
par(PAR) # reset graphics state
# Finally, write the tree to console in Newick format
ape::write.tree(apsTree)
# == 2.1 Rooting Trees =====================================================
# == 3.1 Rooting Trees =====================================================
# In order to analyse the tree, it is helpful to root it first and reorder its
# clades. Contrary to documentation, Rproml() returns an unrooted tree.
@ -163,7 +189,7 @@ plot(apsTree)
ape::nodelabels(cex = 0.5, frame = "circle")
ape::tiplabels(cex = 0.5, frame = "rect")
# The outgroup of the tree is tip "11" in my sample tree, it may be a different
# The outgroup of the tree (KILA ESCCO) is tip "11" in my sample tree, it may be a different
# number in yours. Substitute the correct node number below for "outgroup".
apsTree <- ape::root(apsTree, outgroup = 11, resolve.root = TRUE)
plot(apsTree)
@ -193,7 +219,7 @@ plot(apsTree, cex = 0.7, root.edge = TRUE)
ape::nodelabels(text = "MRCA", node = 12, cex = 0.5, adj = 0.8, bg = "#ff8866")
# == 2.2 Rotating Clades ===================================================
# == 3.2 Rotating Clades ===================================================
# To interpret the tree, it is useful to rotate the clades so that they appear
# in the order expected from the cladogram of species.
@ -206,30 +232,66 @@ plot(ape::rotate(apsTree, node = 13), no.margin = TRUE, root.edge = TRUE)
ape::nodelabels(node = 13, cex = 0.7, bg = "#88ff66")
# Note that the species at the bottom of the clade descending from node
# 17 is now plotted at the top.
layout(matrix(1), widths = 1.0, heights = 1.0)
# ... or we can plot the tree so it corresponds as well as possible to a
# predefined tip ordering. Here we use the ordering that phyloT has returned
# for the species tree.
par(PAR) # reset graphics state
# (Nb. we need to reverse the ordering for the plot. This is why we use the
# expression [nOrg:1] below instead of using the vector directly.)
# ... or we can rearrange the tree so it corresponds as well as possible to a
# predefined tip ordering. Here we use the ordering that taxize:: has inferred
# from the NCBI taxonomic classification.
nOrg <- length(apsTree$tip.label)
layout(matrix(1:2, 1, 2))
plot(fungiTree,
no.margin = TRUE, root.edge = TRUE)
no.margin = FALSE, root.edge = TRUE)
ape::nodelabels(text = fungiTree$node.label,
cex = 0.5,
adj = 0.2,
bg = "#D4F2DA")
plot(ape::rotateConstr(apsTree, apsTree$tip.label[nOrg:1]),
# These are the fungi tree tips ...
fungiTree$tip.label
# ... and their order is determined by the edge-list that is stored in
fungiTree$edge
# which edges join the tips?
ape::tiplabels(cex = 0.5, frame = "rect")
# as you can see, the tips (range [1:nOrg] ) are in column 2 and they are
# ordered from bottom to top.
# And each tip number is the index of the species in the tip.label vector. So we can take column 2, subset it, and use it to get a list of species in the order of the tree ...
sel <- fungiTree$edge[ , 2 ] <= nOrg
( oSp <- fungiTree$tip.label[fungiTree$edge[sel , 2 ]] )
# Now, here are the genes of the apsTree tips ...
apsTree$tip.label
# ... and the "constraint" we need for reordering, according to the help page
# of ape::rotateConstr(), is "a vector specifying the order of the tips as they
# should appear (from bottom to top)". Thus we need to add the "MBP1_" prefix to our vector
oSp <- gsub("^", "MBP1_", oSp)
( oSp <- gsub("MBP1_ESSCO", "KILA_ESCCO", oSp) )
# Then we can plot the two trees to compare: the fungi- tree
par(PAR) # reset graphics state
layout(matrix(1:2, 1, 2))
plot(fungiTree,
no.margin = TRUE,
root.edge = TRUE)
ape::nodelabels(text = fungiTree$node.label,
cex = 0.5,
adj = 0.2,
bg = "#D4F2DA")
# and the re-organized apsesTree ...
plot(ape::rotateConstr(apsTree, constraint = oSp[]),
no.margin = TRUE,
root.edge = TRUE)
ape::add.scale.bar(length = 0.5)
layout(matrix(1), widths = 1.0, heights = 1.0)
par(PAR) # reset graphics state
# As you can see, the reordering is not perfect, since the topologies are
# different, mostly due to the unresolved nodes in the reference tree. One
# could play with that ...
# Task: Study the two trees and consider their similarities and differences.
# What do you expect? What do you find? Note that this is not a "mixed"
@ -240,11 +302,11 @@ layout(matrix(1), widths = 1.0, heights = 1.0)
# branches would you need to remove and reinsert elsewhere to get the
# same topology as the species tree?
# In order to quantiofy how different these tow trees are, we need to compute
# In order to quantify how different these two trees are, we need to compute
# tree distances.
# == 2.3 Computing tree distances ==========================================
# == 3.3 Computing tree distances ==========================================
# Many superb phylogeny tools are contributed by the phangorn package.
@ -262,6 +324,7 @@ if (! requireNamespace("phangorn", quietly = TRUE)) {
apsTree2 <- apsTree
apsTree2$tip.label <- gsub("(MBP1_)|(KILA_)", "", apsTree2$tip.label)
# phangorn provides several functions to compute tree-differences (and there
# is a _whole_ lot of theory on how to compare trees). treedist() returns the
# "symmetric difference"
@ -280,33 +343,41 @@ ape::rtree(n = length(apsTree2$tip.label), # number of tips
# fungiTree has none, so we can't
# compare them anyway.
# (Note the warning message about non-binary trees; we'll suppress that later
# by wrapping the function call in supressMessages(); we don't want to
# print it 10,000 times :-)
# Let's compute some random trees this way, calculate the distances to
# fungiTree, and then compare the values we get for apsTree2. The random
# trees are provided by ape::rtree().
N <- 10000 # takes about 15 seconds
N <- 10000 # takes about 15 seconds, and we'll use the pBar function,
# defined in .utilities.R to keep track of where we are at:
myTreeDistances <- matrix(numeric(N * 2), ncol = 2)
colnames(myTreeDistances) <- c("symm", "path")
set.seed(112358)
for (i in 1:N) {
pBar(i, N)
xTree <- ape::rtree(n = length(apsTree2$tip.label),
rooted = TRUE,
tip.label = apsTree2$tip.label,
br = NULL)
myTreeDistances[i, ] <- phangorn::treedist(fungiTree, xTree)
myTreeDistances[i, ] <- suppressMessages(phangorn::treedist(fungiTree, xTree))
}
set.seed(NULL) # reset the random number generator
table(myTreeDistances[, "symm"])
(symmObs <- phangorn::treedist(fungiTree, apsTree2)[1])
( symmObs <- phangorn::treedist(fungiTree, apsTree2)[1] )
# Random events less-or-equal to observation, divided by total number of
# events gives us the empirical p-value.
cat(sprintf("\nEmpirical p-value for symmetric diff. of observed tree is %1.4f\n",
(sum(myTreeDistances[ , "symm"] <= symmObs) + 1) / (N + 1)))
par(PAR) # reset graphics state
hist(myTreeDistances[, "path"],
col = "aliceblue",
main = "Distances of random Trees to fungiTree")