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variable name typo

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hyginn 2017-11-23 00:32:13 -05:00
parent 8ac1582514
commit 75c6efe4a6
1 changed files with 31 additions and 30 deletions
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BIN-PHYLO-Tree_analysis.R
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@ -3,12 +3,13 @@
# Purpose: A Bioinformatics Course: # Purpose: A Bioinformatics Course:
# R code accompanying the BIN-PHYLO-Tree_analysis unit. # R code accompanying the BIN-PHYLO-Tree_analysis unit.
# #
# Version: 1.0.1 # Version: 1.0.2
# #
# Date: 2017 10 31 # Date: 2017 10 31
# Author: Boris Steipe (boris.steipe@utoronto.ca) # Author: Boris Steipe (boris.steipe@utoronto.ca)
# #
# Versions: # Versions:
# 1.0.2 Typo in variable name, style changes
# 1.0.1 Wrong section heading # 1.0.1 Wrong section heading
# 1.0 First 2017 version # 1.0 First 2017 version
# 0.1 First code copied from 2016 material. # 0.1 First code copied from 2016 material.
@ -29,17 +30,17 @@
#TOC> ========================================================================== #TOC> ==========================================================================
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> ------------------------------------------- #TOC> --------------------------------------------
#TOC> 1 ___Section___ 38 #TOC> 1 Preparation and Tree Plot 43
#TOC> 2 Tree Analysis 77 #TOC> 2 Tree Analysis 82
#TOC> 2.1 Rooting Trees 136 #TOC> 2.1 Rooting Trees 141
#TOC> 2.2 Rotating Clades 182 #TOC> 2.2 Rotating Clades 187
#TOC> 2.3 Computing tree distances 229 #TOC> 2.3 Computing tree distances 234
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
# = 1 Preparation and Tree Plot ============================================ # = 1 Preparation and Tree Plot ===========================================
if (!require(Rphylip, quietly=TRUE)) { if (!require(Rphylip, quietly=TRUE)) {
@ -71,8 +72,8 @@ for (i in seq_along(fungiTree$tip.label)) {
} }
# Plot the tree # Plot the tree
plot(fungiTree, cex=1.0, root.edge=TRUE, no.margin=TRUE) plot(fungiTree, cex = 1.0, root.edge = TRUE, no.margin = TRUE)
nodelabels(text=orgTree$node.label, cex=0.6, adj=0.2, bg="#D4F2DA") nodelabels(text = fungiTree$node.label, cex = 0.6, adj = 0.2, bg = "#D4F2DA")
# Note that you can use the arrow buttons in the menu above the plot to scroll # Note that you can use the arrow buttons in the menu above the plot to scroll
# back to plots you have created earlier - so you can reference back to the # back to plots you have created earlier - so you can reference back to the
# species tree. # species tree.
@ -102,15 +103,15 @@ nodelabels(text=orgTree$node.label, cex=0.6, adj=0.2, bg="#D4F2DA")
load(file = "APSEStreeRproml.RData") load(file = "APSEStreeRproml.RData")
plot(apsTree) # default type is "phylogram" plot(apsTree) # default type is "phylogram"
plot(apsTree, type="unrooted") plot(apsTree, type = "unrooted")
plot(apsTree, type="fan", no.margin = TRUE) plot(apsTree, type = "fan", no.margin = TRUE)
# rescale to show all of the labels: # rescale to show all of the labels:
# record the current plot parameters by assigning them to a variable ... # record the current plot parameters by assigning them to a variable ...
(tmp <- plot(apsTree, type="fan", no.margin = TRUE, plot=FALSE)) (tmp <- plot(apsTree, type="fan", no.margin = TRUE, plot=FALSE))
# ... and adjust the plot limits for a new plot: # ... and adjust the plot limits for a new plot:
plot(apsTree, plot(apsTree,
type="fan", type = "fan",
x.lim = tmp$x.lim * 1.8, x.lim = tmp$x.lim * 1.8,
y.lim = tmp$y.lim * 1.8, y.lim = tmp$y.lim * 1.8,
cex = 0.8, cex = 0.8,
@ -150,8 +151,8 @@ is.rooted(apsTree)
plot(apsTree) plot(apsTree)
# add labels for internal nodes and tips # add labels for internal nodes and tips
nodelabels(cex=0.5, frame="circle") nodelabels(cex = 0.5, frame = "circle")
tiplabels(cex=0.5, frame="rect") 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 is tip "11" in my sample tree, it may be a different
# number in yours. Substitute the correct node number below for "outgroup". # number in yours. Substitute the correct node number below for "outgroup".
@ -170,8 +171,8 @@ apsTree$edge.length
# to show how it connects to the tree without having an # to show how it connects to the tree without having an
# overlap. # overlap.
apsTree$edge.length[1] <- 0.1 apsTree$edge.length[1] <- 0.1
plot(apsTree, cex=0.7) plot(apsTree, cex = 0.7)
nodelabels(text="MRCA", node=12, cex=0.5, adj=0.1, bg="#ff8866") nodelabels(text = "MRCA", node = 12, cex = 0.5, adj = 0.1, bg = "#ff8866")
# This procedure does however not assign an actual length to a root edge, and # This procedure does however not assign an actual length to a root edge, and
@ -179,8 +180,8 @@ nodelabels(text="MRCA", node=12, cex=0.5, adj=0.1, bg="#ff8866")
# myself that too. We'll just add a length by hand. # myself that too. We'll just add a length by hand.
apsTree$root.edge <- mean(apsTree$edge.length) * 1.5 apsTree$root.edge <- mean(apsTree$edge.length) * 1.5
plot(apsTree, cex=0.7, root.edge=TRUE) plot(apsTree, cex = 0.7, root.edge = TRUE)
nodelabels(text="MRCA", node=12, cex=0.5, adj=0.8, bg="#ff8866") nodelabels(text = "MRCA", node = 12, cex = 0.5, adj = 0.8, bg = "#ff8866")
# == 2.2 Rotating Clades =================================================== # == 2.2 Rotating Clades ===================================================
@ -190,13 +191,13 @@ nodelabels(text="MRCA", node=12, cex=0.5, adj=0.8, bg="#ff8866")
# We can either rotate around individual internal nodes ... # We can either rotate around individual internal nodes ...
layout(matrix(1:2, 1, 2)) layout(matrix(1:2, 1, 2))
plot(apsTree, no.margin=TRUE, root.edge=TRUE) plot(apsTree, no.margin = TRUE, root.edge = TRUE)
nodelabels(node=17, cex=0.7, bg="#ff8866") nodelabels(node = 17, cex = 0.7, bg = "#ff8866")
plot(rotate(apsTree, node=17), no.margin=TRUE, root.edge=TRUE) plot(rotate(apsTree, node = 17), no.margin = TRUE, root.edge = TRUE)
nodelabels(node=17, cex=0.7, bg="#88ff66") nodelabels(node = 17, cex = 0.7, bg = "#88ff66")
# Note that the species at the bottom of the clade descending from node # Note that the species at the bottom of the clade descending from node
# 17 is now plotted at the top. # 17 is now plotted at the top.
layout(matrix(1), widths=1.0, heights=1.0) layout(matrix(1), widths = 1.0, heights = 1.0)
# ... or we can plot the tree so it corresponds as well as possible to a # ... or we can plot the tree so it corresponds as well as possible to a
# predefined tip ordering. Here we use the ordering that phyloT has returned # predefined tip ordering. Here we use the ordering that phyloT has returned
@ -209,13 +210,13 @@ nOrg <- length(apsTree$tip.label)
layout(matrix(1:2, 1, 2)) layout(matrix(1:2, 1, 2))
plot(fungiTree, plot(fungiTree,
no.margin=TRUE, root.edge=TRUE) no.margin = TRUE, root.edge = TRUE)
nodelabels(text=fungiTree$node.label, cex=0.5, adj=0.2, bg="#D4F2DA") nodelabels(text = fungiTree$node.label, cex = 0.5, adj = 0.2, bg = "#D4F2DA")
plot(rotateConstr(apsTree, apsTree$tip.label[nOrg:1]), plot(rotateConstr(apsTree, apsTree$tip.label[nOrg:1]),
no.margin=TRUE, root.edge=TRUE) no.margin = TRUE, root.edge = TRUE)
add.scale.bar(length=0.5) add.scale.bar(length = 0.5)
layout(matrix(1), widths=1.0, heights=1.0) layout(matrix(1), widths = 1.0, heights = 1.0)
# Task: Study the two trees and consider their similarities and differences. # 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" # What do you expect? What do you find? Note that this is not a "mixed"