Package 'phecodemap'

Title: Visualization for Phecode Mapping with ICD-9 and ICD-10-cm Codes
Description: Phecodemap builds a shiny app to visualize the hierarchy of Phecode Mapping with ICD. The same Phecode hierarchy is displayed in two ways: as a sunburst plot and as a tree.
Authors: Parse Health [cre, aut]
Maintainer: Parse Health <[email protected]>
License: GPL (>= 3)
Version: 0.2.0
Built: 2025-01-05 05:04:15 UTC
Source: https://github.com/celehs/phecodemap

Help Index

Information of ICD codes

Description

A datatable of the information of icd codes from UMLS version 2021AB

Usage

dict_icd

Format

A data frame with 99765 rows and 3 columns:

id

ICD code

term

ICD string

version

ICD version, ICD-9 or ICD-10-cm

Source

https://uts.nlm.nih.gov/uts/umls/

Mappings of Phecodes to ICD codes.

Description

A dataset containing the mappings of Phecodes to ICD-9 and ICD-10-cm Codes.

Usage

icdmap

Format

A data frame with 106393 rows and 6 variables:

ICD_version

ICD version, ICD-9 or ICD-10-cm

ICD_id

ICD-9 and ICD-10-cm Codes

ICD_str

Description of ICD Codes

Phecode

Phecode ID

Phenotype

Description of Phecode ID

Rollup

Rollup

Source

https://phewascatalog.org/

Run the Shiny Application

Description

Run the Shiny Application

Usage

run_app(
  Uniq_id = NULL,
  url_va = NULL,
  onStart = NULL,
  options = list(),
  enableBookmarking = "server",
  uiPattern = "/",
  ...
)

Arguments

Uniq_id

path to a csv files for dict_uqid.
url_va

url to va for phecode.
onStart

A function that will be called before the app is actually run. This is only needed for shinyAppObj, since in the shinyAppDir case, a global.R file can be used for this purpose.
options

Named options that should be passed to the runApp call (these can be any of the following: "port", "launch.browser", "host", "quiet", "display.mode" and "test.mode"). You can also specify width and height parameters which provide a hint to the embedding environment about the ideal height/width for the app.
enableBookmarking

Can be one of "url", "server", or "disable". The default value, NULL, will respect the setting from any previous calls to enableBookmarking(). See enableBookmarking() for more information on bookmarking your app.
uiPattern

A regular expression that will be applied to each GET request to determine whether the ui should be used to handle the request. Note that the entire request path must match the regular expression in order for the match to be considered successful.
...

arguments to pass to golem_opts. See '?golem::get_golem_options' for more details.