from phycas.Utilities.PDFTree import PDFTree # This example plots the trees in compilation.tre all to the same scale, saving # the result in compilation.pdf (one tree per page) # The PDFTree class is used for this (note that the word plotter is arbitrary) plotter = PDFTree() # Specify the filename of the tree file containing the trees to plot plotter.pdf_treefile = 'compilation.tre' # Specify the filename of the PDF file to output plotter.pdf_filename = 'compilation.pdf' # Specify the outgroup taxon to use when plotting trees plotter.pdf_outgroup_taxon = '40 Cyanophora paradoxa' # Unlink horizontal and vertical dimensions so trees that are not as wide # as others can nevertheless be just as tall plotter.keep_xy_proportional = False # Unlink the size of the tip labels from the size of the tree # (i.e. trees that are smaller have the same size tip labels # as trees that are larger) plotter.keep_tip_labels_proportional = False # Create the compilation.pdf file plotter.pdftree()
from phycas import Newick
from phycas.Utilities.PDFTree import PDFTree
pdftree = PDFTree()
pdftree.pdf_newick = Newick("('P. fimbriata':0.1,('P. articulata':0.09,'P. parksii':0.04)v:0.1,('P. macrophylla':0.14,(('P. gracilis':0.08,('P. ciliata':0.02,'P. basiramia':0.03)x:0.05)y:0.01,'P. polygama':0.09)z:0.06)w:0.07)u", Newick.TAXA_NAMES)
pdftree.pdf_outgroup_taxon = 'P. macrophylla' # use None to display tree as is
pdftree.pdf_tip_label_font = 'Times-Italic' # must be one of the 14 standard font names
pdftree.pdf_tip_label_height = 24 # in units of points
pdftree.pdf_scalebar_label_font = 'Times-Roman' # must be one of the 14 standard font names
pdftree.pdf_scalebar_label_height = 10 # in units of points
pdftree.pdf_ladderize = 'right' # valid choices: None, 'left', or 'right'
pdftree.pdf_scalebar_position = 'bottom' # value choices: None, 'top', or 'bottom'
pdftree.pdf_page_width = 8.5 # in units of inches
pdftree.pdf_page_height = 11.0 # in units of inches
pdftree.pdf_line_width = 2.0 # in units of points
pdftree.pdf_left_margin = 1.0 # in units of inches
pdftree.pdf_right_margin = 1.0 # in units of inches
pdftree.pdf_top_margin = 1.0 # in units of inches
pdftree.pdf_bottom_margin = 1.0 # in units of inches
pdftree.pdf_filename = 'test.pdf'
pdftree.pdftree()
