asPhylo: Convert a data frame to a phylo object

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

Description

asPhylo converts a data frame to a phylo object. Compared to toTree, asPhylo allows the output tree to have different number of nodes in paths connecting leaves to the root.

Usage

asPhylo(data, column_order = NULL, asNA = 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.
asNA	This specifies strings that are considered as NA

Details

The last column is used as the leaf nodes

Value

a phylo object

Author(s)

Ruizhu Huang

Examples

library(ggtree)

# Example 0:
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
taxTree <- asPhylo(data = taxTab)
ggtree(taxTree) + 
 geom_text2(aes(label = label), color = "red", vjust = 1) + 
 geom_nodepoint()
 
 # (Below gives the same output as toTree)
 taxTab$R1 <- paste0("R1:", taxTab$R1)
 taxTab$R2 <- paste0("R2:", taxTab$R2)
 taxTree <- asPhylo(data = taxTab)
# viz the tree           
 ggtree(taxTree) + 
 geom_text2(aes(label = label), color = "red", vjust = 1) + 
 geom_nodepoint()
 
# Example 1
df1 <- rbind.data.frame(c("root", "A1", "A2", NA),
                        c("root", "B1", NA, NA))
colnames(df1) <- paste0("L", 1:4)
tree1 <- asPhylo(df1)

ggtree(tree1, color = "grey") +
geom_nodepoint() +
   geom_text2(aes(label = label), angle = 90,
               color = "red", vjust = 2,
               size = 4)
               
# Example 2
df2 <- data.frame(Group_1 = rep("Root", 11),
                  Group_2 = rep(c(13, 21), c(9, 2)),
                  Group_3 = rep(c(14, 18, "unknown"), c(5, 4, 2)),
                  Group_4 = rep(c(15, "unknown", 19, "unknown"), c(4, 1, 3, 3)),
                  Group_5 = rep(c(16, "unknown", 20, "unknown"), c(3, 2, 2, 4)),
                  Group_6 = rep(c(17, "unknown"), c(2, 9)),
                  LEAF = 1:11)
                  
tree2 <- asPhylo(df2, asNA = "unknown")

ggtree(tree2, color = "grey") +
geom_nodepoint() +
   geom_text2(aes(label = label), angle = 90,
               color = "red", vjust = 2,
               size = 4) 
               
# Example 3
df3 <- df2
df3[10:11, 3] <- ""                                            
 
tree3 <- asPhylo(df3, asNA = c("unknown", ""))

ggtree(tree3, color = "grey") +
geom_nodepoint() +
   geom_text2(aes(label = label), angle = 90,
               color = "red", vjust = 2,
               size = 4) 

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