TaxCIplot: TaxCI plotting
In eberlejonas/TaxCI: Calculate the Consistency Index and the Retention Index for taxonomic data

Description Usage Arguments Value Note Author(s) See Also

Plot the results of a taxonomic consistency analysis with pretty boxes on a tree.

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TaxCIplot(tree, x, plotParamTCI.result, plotParamBCC.result=NA,
      box.placement="auto", adj=.515, step=0.01, label.offset=0.08,
      npages=1, draft=F, vis.clusters=TRUE, info="", legend=FALSE, alternative.tip.labels=NULL, ...)

The arguments must be exactly the same that were used in the tci and the BCCluster analyses:

`tree`	The tree.
`x`	The table with taxonomic information.
`plotParamTCI.result`	The output of `plotParamTCI`.
`plotParamBCC.result`	The output of `plotParamBCC`.
`box.placement`	If set to "auto", TaxCIplot will try to place the boxes in the correct place automatically. EXPERIMENTAL!
`adj`	The offset of the boxes from the tips of the tree. Ignored if `box.placement = "auto"`.
`step`	The step-length to go right before the next box is plotted. Ignored if `box.placement = "auto"`.
`label.offset`	Distance from tips to tip labels. Passed to `plot.phylo` and ignored if `box.placement = "auto"`.
`npages`	The number of pages on which the plot should be distributed. Some tips can be plotted again after page-break. Control this with the margin width options of `par`.
`draft`	Only the first 3 pages are printed. Usefull to adjust spacing in large plots.
`vis.clusters`	Logical: Should small black dots be plotted on nodes of the inferred clusters from `plotParamBCC`? Or alternatively a numeric vector containing the node numbers to plot the dots on.
`alternative.tip.labels`	A vector of mode character or expression and the same length as `tree$tip.labels`. Defaults to NULL (ignored)
`info`	A character string to be plotted at the top right corner of each page. No info is plotted if `info=NA` (default).
`legend`	Logical. Should a legend be plotted?
`...`	Passed to `plot.phylo`. `x.lim` usefull for increasing the plot region to the right (only if `box.placement != "auto"`). Don't use ylim! It's used for multipage-plotting.