View source: R/phyloscan.fun.plotting.R
phsc.plot.phy.selected.individuals | R Documentation |
This function plots short read phylogenies and highlights the clades of two individuals in red and blue.
phsc.plot.phy.selected.individuals(
phs,
dfs,
ids,
plot.cols = rainbow(length(ids)),
plot.file = NA,
group.redo = FALSE,
drop.less.than.n.ids = 2,
drop.blacklisted = FALSE,
pdf.h = 50,
pdf.rw = 10,
pdf.ntrees = 20,
pdf.title.size = 40
)
phs |
List of trees in ape format |
dfs |
data.table with mandatory column 'IDX' and optional column 'TITLE'. IDX is the index of all phylogenies in 'phs' that are to be plotted. TITLE is a title for each sub-plot, for example specifying a window. |
ids |
Vector of regular expressions that identify individuals to be highlighted in colour. |
plot.cols |
Vector of colours for each individual |
plot.file |
If not missing, the phylogenies will be printed to file. |
group.redo |
Logical, indicating if the colour groups should be recalculated from ids. |
drop.blacklisted |
Logical, indicating if all blacklisted taxa should be dropped prior to plotting. |
pdf.h |
Height of the pdf file in inches. |
pdf.rw |
Relative width of the pdf file, internally multiplied by the number of phylogenies to give the total width in inches. |
pdf.ntrees |
Number of trees per pdf. |
pdf.title.size |
Size of pdf title in inches. |
List of ggtree objects, ready for printing.
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