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