R/phyloscan.fun.plotting.R
phsc.plot.phycollapsed.selected.individuals.Rd
This function plots short read phylogenies and highlights the clades of two individuals in red and blue.
phsc.plot.phycollapsed.selected.individuals(phs, dfs, ids, plot.cols = rainbow(length(ids)), plot.cols.background = function(n) { rainbow_hcl(n, start = 60, end = 240, c = 30, l = 80) }, drop.blacklisted = TRUE, tip.regex = "(.*)_read_([0-9]+)_count_([0-9]+)", plot.file = NA, drop.less.than.n.ids = 2, pdf.h = 50, pdf.rw = 10, pdf.ntrees = 20, pdf.title.size = 40)
phs | List of trees in ape format |
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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 |
drop.blacklisted | Logical, indicating if all blacklisted taxa should be dropped prior to plotting. |
plot.file | If not missing, the phylogenies will be printed to file. |
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. |
group.redo | Logical, indicating if the colour groups should be recalculated from ids. |
List of ggtree objects, ready for printing.