View source: R/phyloscan.fun.plotting.R
phsc.plot.phy.selected.pairs | R Documentation |
This function plots short read phylogenies and highlights the clades of two individuals in red and blue.
phsc.plot.phy.selected.pairs(
phs,
dfs,
id1,
id2,
plot.file = NA,
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. |
id1 |
Regular expression that identifies the first individual, to be plotted in red. |
id2 |
Regular expression that identifies the first individual, to be plotted in blue. |
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. |
List of ggtree objects, ready for printing.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.