Description Usage Arguments Value Examples
View source: R/MatchHierPageToEOLdata.R
These functions match hierarchy concept IDs with EOL page data and/or taxonomic tree tips.
1 2 | MatchHierPageToEOLdata(MyHiers, EOLdata)
MatchDataToTreeTips(Tree, Data)
|
MyHiers |
A vector of filenames for downloaded hierarchy pages or a list of XML data stored as an R object |
EOLdata |
Any output dataframe from Reol functions |
Tree |
Taxonomic tree in the class phylo |
Data |
Data output from one of the EOL or Hierarchy gathering functions |
MatchHierPageToEOLdata
returns a data frame where each row is a taxonomic unit. This is especially helpful if you wish to plot EOL data on a taxonomic tree (see example), because it matches the hierarchy taxon names with the EOL data (since taxon names will not always match). MatchDataToTreeTips
will match the tip labels on a tree with those from a data frame. It orders the data in the same way as is in the trees, so that you can plot data on a tree without distortion (either in number of data points, or in taxonomic name).
1 2 3 4 5 6 7 8 9 10 11 12 | #plotting richness scores
## Not run: data(MyEOLs)
library(ape)
data(MyHiers)
Tree <- MakeHierarchyTree(MyHiers, includeNodeLabels=FALSE)
MyData <- MatchHierPageToEOLdata(MyHiers, GetRichnessScores(MyEOLs))
plot(Tree, label.offset=1, x.lim=10)
tiplabels(round(as.numeric(MyData[,3])), 1:6, col="Blue", frame="none",
bg="clear",adj = -0.5)
title(main="Richness scores")
## End(Not run)
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