View source: R/other_useful_functions.R

plotPhyloTree | R Documentation |

Function to plot phylogenetic tree from the estimated results

```
plotPhyloTree(
estPhyloRes,
traitName = NULL,
blockName = NULL,
plotTree = TRUE,
subpopInfo = estPhyloRes$subpopInfo,
saveName = NULL,
saveStyle = "png",
pchBase = c(1, 16),
colNodeBase = c(2, 4),
colTipBase = c(3, 5, 6),
cexMax = 2,
cexMin = 0.7,
edgeColoring = TRUE,
tipLabel = TRUE,
ggPlotTree = FALSE,
cexMaxForGG = 0.12,
cexMinForGG = 0.06,
alphaBase = c(0.9, 0.3)
)
```

`estPhyloRes` |
The estimated results of phylogenetic analysis by 'estPhylo' function for one |

`traitName` |
Name of trait of interest. This will be used in the title of the plots. |

`blockName` |
You can specify the haplotype block (or gene set, SNP-set) of interest by the name of haplotype block in 'geno'. This will be used in the title of the plots. |

`plotTree` |
If TRUE, the function will return the plot of phylogenetic tree. |

`subpopInfo` |
The information of subpopulations. |

`saveName` |
When drawing any plot, you can save plots in png format. In saveName, you should substitute the name you want to save. When saveName = NULL, the plot is not saved. |

`saveStyle` |
This argument specifies how to save the plot of phylogenetic tree. The function offers 'png', 'pdf', 'jpg', and 'tiff'. |

`pchBase` |
A vector of two integers specifying the plot types for the positive and negative genotypic values respectively. |

`colNodeBase` |
A vector of two integers or chracters specifying color of nodes for the positive and negative genotypic values respectively. |

`colTipBase` |
A vector of integers or chracters specifying color of tips for the positive and negative genotypic values respectively. The length of the vector should equal to the number of subpopulations. |

`cexMax` |
A numeric specifying the maximum point size of the plot. |

`cexMin` |
A numeric specifying the minimum point size of the plot. |

`edgeColoring` |
If TRUE, the edge branch of phylogenetic tree wiil be colored. |

`tipLabel` |
If TRUE, lavels for tips will be shown. |

`ggPlotTree` |
If TRUE, the function will return the ggplot version of phylogenetic tree. It offers the precise information on subgroups for each haplotype. |

`cexMaxForGG` |
A numeric specifying the maximum point size of the plot for ggtree, relative to the range of x and y-axes (0 < cexMaxForGG <= 1). |

`cexMinForGG` |
A numeric specifying the minimum point size of the plot for ggtree, relative to the range of x and y-axes (0 < cexMaxForGG <= 1). |

`alphaBase` |
alpha (parameter that indicates the opacity of a geom) for tip with positive / negative effects. alpha for node will be same as the alpha for tip with negative effects. |

Draw plots of phylogenetic tree.

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