toTree: Translate a data frame to a phylo object

In fionarhuang/TreeSummarizedExperiment: TreeSummarizedExperiment: a S4 Class for Data with Tree Structures

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()

fionarhuang/TreeSummarizedExperiment documentation built on Aug. 18, 2021, 12:15 p.m.