Package index • napistu.r

Initialization

Configure a napistu_list object containing a database and network-based representation of a pathway and bindings to the Napistu Python package.

Configuration

object- and yaml-level configuration of the core napistu_list

setup_napistu_list(): Setup Napistu List

create_napistu_config(): Create Napistu Configuration

load_napistu_config(): Load Napistu Configuration from YAML

Assets

loading the core Napistu objects - an sbml_dfs, napistu_graph, species_identifiers and optionally, precomputed_distances

load_assets(): Load Assets

load_single_asset(): Load Single Asset File

Default Python Environment

Setting up and tearing down a conda environment with Napistu installed improve usability and support CI/CD

cleanup_napistu(): Clean Up Napistu Environment

create_conda_environment(): Create Conda Environment

create_default_conda_env(): Create Default Conda Environment

Network Visualization

Approaches for querying and visualizing Napistu graphs.

Subgraphs

Creating an induced subgraph containing a set of vertices of interest and visualizing the resulting weaklyconnected components

define_subgraphs(): Create Subgraph

plot_subgraph(): Plot Subgraphs

plot_one_component(): Plot One Component

Neighborhoods

Creating and plotting the molecular neighborhood of a focal species

create_neighborhood_summary_table(): Create Neighborhood Summary Table

create_neighborhood_table(): Create Neighborhood Table

plot_one_neighborhood(): Plot One Neighborhood

plot_neighborhoods(): Summarize Neighborhoods

Shortest Paths

Find and plot the shortest network paths between two species

find_all_shortest_paths(): Find All Shortest Reaction Paths

plot_shortest_path_network(): Plot Shortest Path Network

summarize_shortest_paths(): Summarize Shortest Paths

Shiny Modules

Interactive Shiny modules for exploring Napistu networks

Shiny Module - Basic Info

shiny_basicInfo_test(): Shiny Basic Info Test

basicInfoInput(): Basic Info Input

basicInfoServer(): Basic Info Server

Shiny Module - Select Entity

shiny_selectEntity_test(): Shiny Select Entity Test

selectEntityInput(): Select Entity Input

selectEntityServer(): Select Entity Server

Shiny Module - Neighborhoods

shiny_neighborhood_test(): Shiny Neighborhood Test

neighborhoodInput(): Neighborhood Input

neighborhoodServer(): Neighborhood Server

Shiny Module - Shortest Paths

shiny_shortestPaths_test(): Shiny Shortest Paths Test

shortestPathsInput(): Shortest Paths Input

shortestPathsServer(): Shortest Paths Server

R-Based Functionality Supporting Napistu Pathway Transformations

These functions are used to pull data and metadata into the Napistu framework. Many of these functions are accessed through the rpy2 module of the Napistu Python package or through its CLI. With time hopefully some or all of these R calls from Python can be replaced with pure Python.

Gene Metadata

Many of the functions in Napistu depend on genic metadata which is currently pulled from specialized species-level Bioconductor packages.

bioconductor_org_function(): Bioconductor Org Function

bioconductor_org_library(): Bioconductor Org Library

bioconductor_org_package_prefix(): Bioconductor Org Package Prefix

Additional Functionality

Lightly supported functionality which is loosly related to Napistu

Open Targets

Functions for pulling data from the Open Targets graphQL API

query_open_targets_targets(): Query Open Targets - Targets

query_open_targets_indications(): Query Open Targets - Indications

shiny_opentargets_test(): Shiny Open Targets Test

summarize_open_targets_targets(): Summarize Open Targets - Targets

summarize_diseases(): Summarize Diseases

summarize_indication(): Summarize Indications

Data

Data which is bundled with napistu-r

efo_diseases: EFO Diseases