Mercurial > repos > boris > phylorelatives
comparison phylorelatives.py @ 42:35741a74d073 draft default tip
type="cairo" added to plotting function
| author | boris |
|---|---|
| date | Wed, 29 Jan 2014 11:05:27 -0500 |
| parents | dd39849c2ff1 |
| children |
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| 41:9453ba52f46b | 42:35741a74d073 |
|---|---|
| 100 def ape_plot_tree(outfile, tree1, root=False): | 100 def ape_plot_tree(outfile, tree1, root=False): |
| 101 """Plot tree to png file""" | 101 """Plot tree to png file""" |
| 102 ape = importr('ape') | 102 ape = importr('ape') |
| 103 graphics = importr('graphics') | 103 graphics = importr('graphics') |
| 104 grdevices = importr('grDevices') | 104 grdevices = importr('grDevices') |
| 105 grdevices.png(file=outfile, width=1024, height=768) | 105 grdevices.png(file=outfile, width=1024, height=768,type="cairo") |
| 106 if root: | 106 if root: |
| 107 tree = ape.root(tree1,root) | 107 tree = ape.root(tree1,root) |
| 108 labels = list(tree.rx("tip.label")[0]) | 108 labels = list(tree.rx("tip.label")[0]) |
| 109 colors = robjects.StrVector(["red" if tip.endswith("_minor") else "black" for tip in labels]) | 109 colors = robjects.StrVector(["red" if tip.endswith("_minor") else "black" for tip in labels]) |
| 110 ape.plot_phylo(tree,tip_color=colors,use_edge_length=0, | 110 ape.plot_phylo(tree,tip_color=colors,use_edge_length=0, |