add_ci | R Documentation |
These are low-level plotting commands to draw the confidence intervals on the node of a tree as rectangles with coloured backgrounds or add boxplots to ultrametric or tipdated trees.
add_ci(tree, trees, col95 = "#FF00004D", col50 = "#0000FF4D",
height = 0.7, legend = TRUE, ...)
add_boxplot(tree, trees, ...)
tree |
a phylogenetic tree to which the confidences should be added. |
trees |
phylogenetic trees, i.e. an object of class 'multiPhylo' |
col95 |
colour used for the 95 red. |
col50 |
colour used for the 50 blue. |
height |
the height of the boxes. |
legend |
a logical value. |
... |
arguments passed to other functions, |
All trees should to be rooted, either ultrametric or tip dated.
Nothing. Function is called for adding to a plot.
Emmanuel Paradis, Santiago Claramunt, Joseph Brown, Klaus Schliep
plot.phylo
, plotBS
,
add_edge_length
, maxCladeCred
data("Laurasiatherian")
dm <- dist.hamming(Laurasiatherian)
tree <- upgma(dm)
set.seed(123)
trees <- bootstrap.phyDat(Laurasiatherian,
FUN=function(x)upgma(dist.hamming(x)), bs=100)
tree <- plotBS(tree, trees, "phylogram")
add_ci(tree, trees, bty="n")
plot(tree, direction="downwards")
add_boxplot(tree, trees, boxwex=.7)
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