Creating treechart from tabbed text in R

Question

I want to make a tree/flowchart of following data which is properly indented with tabs:

Vertebrates
    fish
        goldfish
        clownfish
    amphibian
        frog
        toad
    reptiles
        snake
        lizard
        turtle
        tortoise
    birds
        sparrow
        crow
        parrot
    mammals
        dog
        cat
        horse
        whale

How can I convert this tree data to a flowchart (with arrows going from above downwards or from left to right) (proper position to be determined by counting the number of tabs in each row). I believe it can be done with "diagram" package (Graph flow chart of transition from states , http://cran.r-project.org/web/packages/diagram/index.html) but could not figure out exact steps. Thanks for your help.

A rough sample desired output is given below. There could be boxes around text.

enter image description here

EDIT: It should ideally be a flexible solution so that it works if levels are added or removed. For example adding 2 types of sparrows:

Vertebrates         
    fish        
        goldfish    
        clownfish   
    amphibian       
        frog    
        toad    
    reptiles        
        snake   
        lizard  
        turtle  
        tortoise    
    birds       
        sparrow 
            house
            factory
        crow    
        parrot  
        crane   
    mammals     
        dog 
        cat 
        horse   
        whale   

dat  = structure(list(V1 = c("Vertebrates", NA, NA, NA, NA, NA, NA, 
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 
NA), V2 = c(NA, "fish", NA, NA, "amphibian", NA, NA, "reptiles", 
NA, NA, NA, NA, "birds", NA, NA, NA, NA, NA, NA, "mammals", NA, 
NA, NA, NA), V3 = c(NA, NA, "goldfish", "clownfish", NA, "frog", 
"toad", NA, "snake", "lizard", "turtle", "tortoise", NA, "sparrow", 
NA, NA, "crow", "parrot", "crane", NA, "dog", "cat", "horse", 
"whale"), V4 = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 
NA, NA, NA, "house", "factory", NA, NA, NA, NA, NA, NA, NA, NA
)), .Names = c("V1", "V2", "V3", "V4"), class = "data.frame", row.names = c(NA, 
-24L))
>

It's this more of a tree shape than a flow chart? Maybe like a dendrogram? — MrFlick, Jul 23 '14 at 17:50

user20650 · Accepted Answer · 2014-07-24T03:30:17.353

This is a rather convoluted way using igraph. We need to arrange your data in to two columns, from and to indicating an arrow from -> to.

library(zoo)
library(igraph)

# read tab delimited data - keep structure by setting "" to missing
# (would of been great if you had given this in a format easier to use)

dat <- read.table("test.txt", sep="\t", header=FALSE, fill=TRUE, 
                  na.strings="", strip.white=TRUE, stringsAsFactors=FALSE)

head(dat, 7)
#             V1        V2        V3
#1   Vertebrates      <NA>      <NA>
#2          <NA>      fish      <NA>
#3          <NA>      <NA>  goldfish
#4          <NA>      <NA> clownfish
#5          <NA> amphibian      <NA>
#6          <NA>      <NA>      frog
#7          <NA>      <NA>      toad

Prepare data to graph

# carry forward the last value in first two columns to impute missing
dat[1:2] <- sapply(dat[1:2], na.locf, na.rm=FALSE)
dat <- na.omit(dat)

# get edges for graph - we want two columns (from and to) for each edges
edges <- rbind(dat[1:2],setNames(dat[2:3],names(dat[1:2])))

# create graph
g <- graph.data.frame(edges)

# Plot graph
E(g)$curved <- 0
plot.igraph(g, vertex.size=0, edge.arrow.size=0 ,
                      layout=-layout.reingold.tilford(g)[,2:1])

data as there will be better ways to do this!!

dat <- structure(list(V1 = c("Vertebrates", NA, NA, NA, NA, NA, NA, 
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA), V2 = c(NA, 
"fish", NA, NA, "amphibian", NA, NA, "reptiles", NA, NA, NA, 
NA, "birds", NA, NA, NA, "mammals", NA, NA, NA, NA), V3 = c(NA, 
NA, "goldfish", "clownfish", NA, "frog", "toad", NA, "snake", 
"lizard", "turtle", "tortoise", NA, "sparrow", "crow", "parrot", 
NA, "dog", "cat", "horse", "whale")), .Names = c("V1", "V2", 
"V3"), class = "data.frame", row.names = c(NA, -21L))

EDIT : Update following new data

Calling your updated datadat2

# To prepare the data

# carry forward the last value in columns if lower level (col to the right)
# is non-missing
dat2[1] <- na.locf(dat2[1], na.rm=FALSE)

for(i in ncol(dat2):2)  {
  dat2[[i-1]] <-  ifelse(!is.na(dat2[[i]]), na.locf(dat2[[i-1]], na.rm=F), 
                                                                   dat2[[i-1]])
      }            

# get edges for graph
edges <- rbind(na.omit(dat2[1:2]),
                       do.call('rbind',
                               lapply(1:(ncol(dat2)-2), function(i) 
                                  na.omit(setNames(dat2[(1+i):(2+i)],
                                                         names(dat2[1:2])))))
                         )

Then continue as before, to give

enter image description here

Thanks, it works well for this data but does not work if I add another level, say 2 types of sparrows: house, factory. Can we create a function which automatically adjusts for this? — rnso, Jul 24 '14 at 01:44
Could you edit your question to add a small example of the more complex data please. If you use `dput(yourdata)` you will get the data in the same format as at the end of my answer - makes it a lot easier, cheers — user20650, Jul 24 '14 at 01:50
@mso; updated - should be easy to make a (ugly) function from this - HTH — user20650, Jul 24 '14 at 03:25
It works very well. However, if I change the order of entries, sometimes the order displayed on graph is different. — rnso, Jul 24 '14 at 04:19
Please see follow-up question: http://stackoverflow.com/questions/24948003/order-of-flowchart-treemap-entries-not-correct-in-r-igraph-package — rnso, Jul 25 '14 at 05:56

Creating treechart from tabbed text in R

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