Summarize Neighborhoods
Usage
plot_neighborhoods(
napistu_list,
neighborhood_table,
score_overlay = NULL,
score_label = NULL,
...
)Arguments
- napistu_list
A list containing loaded assets and bindings to Python modules.
- sbml_dfs
SBML_dfs - the core pathway representation of the Napistu Python library
- napistu_graph
Network graph - a Python igraph subclass with Napistu-specific attributes and methods
- species_identifiers
Species identifier mappings
- precomputed_distances
optional, distances between species nodes
- species_names
A tibble containing the names of all genes, proteins, molecules, etc
- identifiers_nest
A tibble with one row per ontology and a nested tibble containing all the identifiers and their corresponding molecular species
- python_modules
A named list of Python modules: `napistu`
- python_environment
- napistu_config
A `napistu_config` object dictating how the `napistu_list` was initialized
- loaded_at
A date-time object indicating when `napistu_list` was initialized
- neighborhood_table
Neighborhood table created by
create_neighborhood_table- score_overlay
optional, vertex-level scores containing `score` and the merging attribute specified in `join_on`
- score_label
optional, name of disease being overlaid
- ...
extra arguments passed to
plot_one_neighborhood
Examples
suppressPackageStartupMessages(library(dplyr))
setup_napistu_list(create_napistu_config())
#>
#> ── Setting up Napistu environment ──────────────────────────────────────────────
#> No Python configuration specified, setting up conda environment
#> Using existing conda environment "napistu-config"
#> Python version 3.11 meets requirements
#> No assets configuration specified, loading bundled package data
#> Loading sbml_dfs from sbml_dfs.pkl
#> Error in value[[3L]](cond): Failed to load sbml_dfs from
#> /home/runner/work/_temp/Library/napistu.r/extdata/test_pathway/sbml_dfs.pkl:
#> ImportError: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: version `OPENSSL_3.3.0'
#> not found (required by
#> /usr/share/miniconda/envs/napistu-config/lib/python3.11/lib-dynload/_ssl.cpython-311-x86_64-linux-gnu.so)
#> Run `reticulate::py_last_error()` for details.
species_id <- random_species(napistu_list)
#> Error: object 'napistu_list' not found
neighborhood_table <- create_neighborhood_table(
napistu_list,
species_id = species_id,
max_steps = 3L,
max_neighbors = 40L,
)
#> Error: object 'napistu_list' not found
# score_overlay <- summarize_indication(
# napistu_list,
# disease_id = "EFO_0000400",
# create_neighborhood_summary_table(neighborhood_table)
# )
score_overlay <- neighborhood_table %>%
dplyr::select(vertices) %>%
tidyr::unnest(vertices) %>%
dplyr::filter(node_type == "species") %>%
dplyr::distinct(s_id) %>%
dplyr::sample_frac(0.5) %>%
dplyr::mutate(score = stats::rnorm(dplyr::n()))
#> Error: object 'neighborhood_table' not found
neighborhood_summaries <- plot_neighborhoods(
napistu_list,
neighborhood_table,
score_overlay,
score_label = "random scores",
score_palette = "log2 fold-change"
)
#> Error: object 'napistu_list' not found