toTree {TreeSummarizedExperiment} | R Documentation

## Translate a data frame to a phylo object

### Description

`toTree` translates a data frame to a phylo object

### Usage

    toTree(data, column_order = NULL)

### Arguments

`data` | A data frame or matrix.
`column_order` | A vector that includes the column names of data to reorder columns of `data`. Default is NULL, the original order of `data` is kept.

### Details

The last column is used as the leaf nodes

### Value

a phylo object

### Author(s)

Ruizhu HUANG

### Examples

    library(ggtree)
    # Example 1:
    taxTab <- data.frame(R1 = rep("A", 5),
                         R2 = c("B1", rep("B2", 4)),
                         R3 = paste0("C", 1:5))
    # Internal nodes: their labels are prefixed with colnames of taxTab
    #  e.g., R2:B2
    tree <- toTree(data = taxTab)
    # viz the tree
     ggtree(tree) +
     geom_text2(aes(label = label), color = "red", vjust = 1) +
     geom_nodepoint()

    # Example 2: duplicated rows in the 3rd and 4th rows
    taxTab <- data.frame(R1 = rep("A", 5),
                         R2 = c("B1", rep("B2", 4)),
                         R3 = c("C1", "C2", "C3", "C3", "C4"))
    # duplicated rows are removed with warnings
    tree <- toTree(data = taxTab)

    # Example 3: NA values in R2 column
    # results: the internal node with the label 'R2:'
    taxTab <- data.frame(R1 = rep("A", 5),
                         R2 = c("B1", rep("B2", 2), NA, "B2"),
                         R3 = c("C1", "C2", "C3", NA, "C4"))
    tree <- toTree(data = taxTab)
    # viz the tree
     ggtree(tree) +
     geom_text2(aes(label = label), color = "red", vjust = 1) +
     geom_nodepoint()

    # Example 4: duplicated values in the leaf column (R4)
    # Not allowed and give errors
    # taxTab <- data.frame(R1 = rep("A", 5),
    #                      R2 = c("B1", rep("B2", 3), "B3"),
    #                      R3 = c("C1", "C2", "C3", "C3",NA),
    #                      R4 = c("D1", "D2", "D3", NA, NA))

    # Example 5: loops caused by missing values in B2-C4, B3-C4
    taxTab <- data.frame(R1 = rep("A", 6),
                         R2 = c("B1", rep("B2", 4), "B3"),
                         R3 = c("C1", "C2", "C3", "C3", "C4", "C4"),
                         R4 = c("D1", "D2", "D3", "D3", "D4" , "D4"),
                         R5 = paste0("E", 1:6))
     # resolove loops before run to Tree
     # Suffix are adding to C4
     taxNew <- resolveLoop(taxTab)
     tree <- toTree(data = taxNew)

     # viz the tree
     ggtree(tree) +
     geom_text2(aes(label = label), color = "red", vjust = 1) +
     geom_nodepoint()

[Package TreeSummarizedExperiment version 2.2.0 Index]