Package {visATC}

visATC: Visualise the Anatomical Therapeutic Chemical (ATC) Hierarchy

Description

Visualisation and subsetting of the World Health Organisation Anatomical Therapeutic Chemical (ATC) classification system.

Author(s)

Maintainer: J Matthews jnmatt212@gmail.com [copyright holder]

See Also

Useful links:

• https://jnm212.github.io/visATC/

nodes of the ATC hierarchy

Description

This contains nodes of the ATC hierarchy at all 5 levels (e.g. A, A01, A01A ...), and associated descriptive text (eg. for A: ALIMENTARY TRACT AND METABOLISM), used here for visualisation.

Usage

ATCdata

Format

A named character vector for each node, where each entry is an ATC code and the name is a textual description

Source

The ATC data can be perused at <https://atcddd.fhi.no/atc_ddd_index/>.

This data is from the repository at <https://github.com/fabkury/atcd> and this release is at <https://github.com/fabkury/atcd/releases/tag/april2026>.

The first two columns from the .csv file were selected to produce the named character vector

find a subset of the tree

Description

find a subset of the tree

Usage

## S4 method for signature 'atctree'
x[i, j = 0]

Arguments

Details

The subset method for objects of class atctree uses a focal node and a specification of how many generations to accrue. The focal node is specified by an ATC code at any of the five levels (e.g. i="A01"). The generation is specified by integer j, signed positive for ancestors and negative for descendants.

Value

an object of class atctree

Examples

h <- atctree(schema="full")
#more useful to use the full tree with this approach
# plot the siblings of C01:
plot(h["C01",0], ATC_text=TRUE, stem_label=TRUE, leaf_label=TRUE)
# plot descendents of P01 (as far as grandchildren):
plot(h["P01",-2], stem_label=TRUE, leaf_label=TRUE)
# plot descendents of P01 (as far as great grandchildren):
plot(h["P01",-3], stem_label=TRUE, leaf_label=TRUE)

constructor for atctree objects

Description

constructor for atctree objects

Usage

atctree(
  whichlevs = NULL,
  schema = c("none", "full", "anatomical", "therapeutic", "chemical")
)

Arguments

Details

either schema or whichlevs should be specified; (e.g. 'schema=full' corresponds to 'whichlevs=1:5')

Value

an object of class atctree

Examples

h <- atctree(schema="anatomical")
# tree will contain levels 1 and 5
h <- atctree(whichlevs=c(1,2,5))
# bespoke structure

class to represent a tree from the ATC hierarchy

Description

class to represent a tree from the ATC hierarchy

Slots

node

node id

pnode

parent node id

lab

ATC code

plab

parent ATC code

text

ATC textual info

lev

level of each node (root node is 0)

schema

one of 'none', 'full', 'anatomical', 'therapeutic', 'chemical'

whichlevs

subset of integers 1:5; should correspond to schema

Nnode

number of nodes in the tree excluding root node

Nlev

number of levels in the tree excluding root node

cutting from an ATC tree

Description

Cut out a branch with just the descendants of the specified node.

This will include the direct parent of the specified node as information - this is also useful for grafting.

Usage

## S4 method for signature 'atctree'
cutting(h, nodelabel = NULL)

Arguments

Value

returns a (smaller) object of class atctree

Examples

h <- atctree(schema="therapeutic")
# Suppose we are interested in a branch of this tree; take a cutting and plot it:
plot(cutting(h, "P01"))

# a different look:
plot(cutting(h, "P01"),  text_angle=0, circle=TRUE)

display drug name for ATC codes

Description

display drug name for ATC codes

Usage

drugnames(x)

Arguments

Value

character vector of drug names

show the parents of the specified node(s)

Description

show the parents of the specified node(s)

Usage

parents(x)

Arguments

Value

character vector

plot the tree as a network graph

Description

plot the tree as a network graph

Usage

## S4 method for signature 'atctree'
plot(
  x,
  circle = NULL,
  ATC_text = NULL,
  leaf_label = NULL,
  stem_label = NULL,
  text_size = 10,
  text_angle = 45,
  width = 500,
  height = 500,
  hover_msg = TRUE
)

Arguments

Details

Each node is labelled with its ATC code, and by hovering the cursor over any node the ATC desciption is displayed. The ATC tree can be displayed as a network in layers or on a circle (with radii corresponding to ATC level). It is evident that a plot the full ATC tree is too cluttered. Some subsetting (link), pruning (link) or cutting (link) of the tree is likely to help visualisation.

Value

No return value, called for side effects

Examples

# create an ATC tree and plot the whole thing:
h <- atctree(schema="full")
# you could plot this with plot(h) but it takes a while 
# large network so not easy to read

# take cutting above node B ; plot all its descendants:
plot(cutting(h,"B"))

# plot siblings of node A03
plot(h["A03",0])

# plot node B down to its grandchildren:
plot(h["B",-2])
# or use a circular layout
plot(h["B",-2], circle=TRUE, stem_label=TRUE)

prune an ATC tree

Description

Pruning is specifying the removal of some unwanted branch of the tree (in contrast to taking a cutting, where it is the branch which is kept).

Usage

## S4 method for signature 'atctree'
pruning(h, nodelabels = NULL)

Arguments

Value

a (smaller) object of class atctree

Examples

library(visATC)
h1 <- atctree(whichlevs=1:3)
h1A <- cutting(h1, "C")
# make a subtree cut at node C
plot(h1A, circle=TRUE)
# suppose we decide not to display some nodes:
plot(pruning(h1A, c("C01", "C05", "C10")), circle=TRUE)

summarise atctree object

Description

shows schema, number of nodes and levels and a cross-table, excluding the root node.

Usage

## S4 method for signature 'atctree'
show(object)

Arguments

Value

prints summary to console

Examples

h <- atctree(whichlevs=1:4)
(h)

helper functions for atctrees

Description

treelevs: return levels within tree (excluding 0)

leaves: return labels of terminal elements (leaves) of tree

nlevs: number of levels in tree (excluding 0)

Usage

## S4 method for signature 'atctree'
treelevs(h)

## S4 method for signature 'atctree'
leaves(h)

## S4 method for signature 'atctree'
nlevs(h)

Arguments

Value

a vector of the level of each node

vector of labels of the leaf nodes

vector of number of levels in the tree