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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)) {
@ -72,7 +73,7 @@ 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.