Tskit and R

Tskit and R#

To interface with tskit in R, we can use the reticulate R package, which lets you call Python functions within an R session. In this tutorial, we’ll go through a couple of examples to show you how to get started. If you haven’t done so already, you’ll need to install reticulate in your R session via install.packages("reticulate").

We’ll begin by simulating a small tree sequence using msprime.

msprime <- reticulate::import("msprime")

ts <- msprime$sim_ancestry(80, sequence_length=1e4, recombination_rate=1e-4, random_seed=42)
ts  # See "Jupyter notebook tips", below for how to render this nicely

╔═══════════════════════════╗
║TreeSequence               ║
╠═══════════════╤═══════════╣
║Trees          │         26║
╟───────────────┼───────────╢
║Sequence Length│      10000║
╟───────────────┼───────────╢
║Time Units     │generations║
╟───────────────┼───────────╢
║Sample Nodes   │        160║
╟───────────────┼───────────╢
║Total Size     │   29.1 KiB║
╚═══════════════╧═══════════╝
╔═══════════╤════╤══════════╤════════════╗
║Table      │Rows│Size      │Has Metadata║
╠═══════════╪════╪══════════╪════════════╣
║Edges      │ 414│  12.9 KiB│          No║
╟───────────┼────┼──────────┼────────────╢
║Individuals│  80│   2.2 KiB│          No║
╟───────────┼────┼──────────┼────────────╢
║Migrations │   0│   8 Bytes│          No║
╟───────────┼────┼──────────┼────────────╢
║Mutations  │   0│  16 Bytes│          No║
╟───────────┼────┼──────────┼────────────╢
║Nodes      │ 344│   9.4 KiB│          No║
╟───────────┼────┼──────────┼────────────╢
║Populations│   1│ 224 Bytes│         Yes║
╟───────────┼────┼──────────┼────────────╢
║Provenances│   1│1015 Bytes│          No║
╟───────────┼────┼──────────┼────────────╢
║Sites      │   0│  16 Bytes│          No║
╚═══════════╧════╧══════════╧════════════╝

Attributes and methods#

reticulate allows us to access a Python object’s attributes via the $ operator. For example, we can access (and assign to a variable) the number of samples in the tree sequence:

n <- ts$num_samples
n
160

The $ operator can also be used to call methods, for example, the simplify() method associated with the tree sequence. The method parameters are given as native R objects (but note that object IDs still use tskit’s 0-based indexing system).

reduced_ts <- ts$simplify(0:7)  # only keep samples with ids 0, 1, 2, 3, 4, 5, 6, 7
reduced_ts <- reduced_ts$delete_intervals(list(c(6000, 10000)))  # delete data after 6kb
reduced_ts <- reduced_ts$trim()  # remove the deleted region
paste(
    "Reduced from", ts$num_trees, "trees over", ts$sequence_length/1e3, "kb to",
    reduced_ts$num_trees, "trees over", reduced_ts$sequence_length/1e3, "kb.")
'Reduced from 26 trees over 10 kb to 6 trees over 6 kb.'

IDs and indexes#

Note that if a bare digit is provided to one of these methods, it will be treated as a floating point number. This is useful to know when calling tskit methods that require integers (e.g. object IDs). For example, the following will not work:

ts$node(0)  # Will raise an error

In this case, to force the 0 to be passed as an integer, you can either coerce it using as.integer or simply prepend the letter L:

ts$node(as.integer(0))
# or
ts$node(0L)

Node(id=0, flags=1, time=0.0, population=0, individual=0, metadata=b'')

Node(id=0, flags=1, time=0.0, population=0, individual=0, metadata=b'')

Coercing in this way is only necessary when passing parameters to those underlying tskit methods that expect integers. It is not needed e.g. to index into numeric arrays. However, when using arrays, very careful attention must be paid to the fact that tskit IDs start at zero, whereas R indexes start at one:

root_id <- ts$first()$root
paste("Root time via tskit method:", ts$node(root_id)$time)
# When indexing into tskit arrays in R, add 1 to the ID
paste("Root time via array access:", ts$nodes_time[root_id + 1])
'Root time via tskit method: 3.4634393266485'
'Root time via array access: 3.4634393266485'

Analysis#

From within R we can use tskit’s powerful Statistics framework to efficiently compute many different summary statistics from a tree sequence. To illustrate this, we’ll first add some mutations to our tree sequence with the msprime.sim_mutations() function, and then compute the genetic diversity for each of the tree sequence’s sample nodes:

ts_mut = msprime$sim_mutations(reduced_ts, rate=1e-4, random_seed=321)

paste(ts_mut$num_mutations, "mutations, genetic diversity is", ts_mut$diversity())
'13 mutations, genetic diversity is 0.000720238095238095'

Numerical arrays and matrices work as expected. For instance, we can use the tree sequence genotype_matrix() method to return the genotypes of the tree sequence as a matrix object in R.

G = ts_mut$genotype_matrix()
G
A matrix: 13 × 8 of type int
00010000
00000010
10000000
00100000
00110110
01110110
01111111
01111111
10000000
00001001
10000000
01110110
00001000

We can then use R functions directly on the genotype matrix:

allele_frequency = rowMeans(G)
allele_frequency
  1. 0.125
  2. 0.125
  3. 0.125
  4. 0.125
  5. 0.5
  6. 0.625
  7. 0.875
  8. 0.875
  9. 0.125
  10. 0.25
  11. 0.125
  12. 0.625
  13. 0.125

Jupyter notebook tips#

When running R within a Jupyter notebook, a few magic functions can be defined that allow tskit objects to be rendered within the notebook:

# Define some magic functions to allow objects to be displayed in R Jupyter notebooks
repr_html.tskit.trees.TreeSequence <- function(obj, ...){obj$`_repr_html_`()}
repr_html.tskit.trees.Tree <- function(obj, ...){obj$`_repr_html_`()}
repr_svg.tskit.drawing.SVGString <- function(obj, ...){obj$`__str__`()}

This leads to much nicer tabular summaries:

ts_mut
Tree Sequence
Trees6
Sequence Length6000.0
Time Unitsgenerations
Sample Nodes8
Total Size6.1 KiB
MetadataNo Metadata
Table Rows Size Has Metadata
Edges 32 1.0 KiB
Individuals 4 136 Bytes
Migrations 0 8 Bytes
Mutations 13 497 Bytes
Nodes 20 568 Bytes
Populations 1 224 Bytes ✅
Provenances 5 3.1 KiB
Sites 13 341 Bytes

It also allows trees and tree sequences to be plotted inline:

ts_mut$draw_svg(y_axis=TRUE, y_ticks=0:10)
_images/171457126272def36ebbbc270193bfc29243eda867dbd1dd6481cd4c8f42611e.svg

Interaction with R libraries#

R has a number of libraries to deal with genomic data and trees. Below we focus on the phylogenetic tree representation defined in the the popular ape package, taking all the trees exported in Nexus format, or individual trees exported in Newick format:

file = tempfile()
ts_mut$write_nexus(file)
# Warning - ape trees are stored independently, so this will use much more memory than tskit
trees <- ape::read.nexus(file, force.multi = TRUE)  # return a set of trees

# Or simply read in a single tree
tree <- ape::read.tree(text=ts_mut$first()$as_newick())

# Now we can plot the tree in tskit style, but using the ape library
plot(tree, direction="downward", srt=90, adj=0.5)  # or equivalently use trees[[1]]
_images/34ebd1f9701ac0dfb3ca74c95abc7d4246121e6dd9b326a5e5ac0bdfa1146daa.png

Note that nodes are labelled with the prefix n, so that nodes 0, 1, 2, … become n0, n1, n2 … etc. This helps to avoid confusion between the the zero-based counting system used natively by tskit, and the one-based counting system used in R.

Further information#

Be sure to check out the reticulate documentation, in particular on Calling Python from R, which includes important information on how R data types are converted to their equivalent Python types.

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