Create interactive network plot start to finish — ggnetwork_plot

This puts all the functions together from getting the subset of results to creating the final interactive plot.

ggnetwork_plot_full(
  filters,
  keep_descendants = NULL,
  results = load_example_results(),
  hpo = HPOExplorer::get_hpo(),
  q_threshold = 5e-04,
  effect_threshold = 1,
  columns = HPOExplorer::list_columns(),
  colour_var = "effect",
  size_var = "ontLvl_relative",
  add_ont_lvl_absolute = TRUE,
  add_ont_lvl_relative = TRUE,
  method = c("ggnetwork", "visnetwork"),
  interactive = TRUE,
  verbose = TRUE,
  ...
)

Arguments

filters

A named list, where each element in the list is the name of a column in the data, and the vector within each element represents the values to include in the final data.

keep_descendants

Terms whose descendants should be kept (including themselves). Set to NULL (default) to skip this filtering step.

results

The cell type-phenotype enrichment results generated by gen_results and merged together with merge_results

hpo

Human Phenotype Ontology object, loaded from get_ontology.

q_threshold

The q value threshold to subset the results by.

effect_threshold

The minimum fold change in specific expression to subset the results by.

columns

A named vector of columns in phenos to add to the hoverdata via add_hoverboxes.

colour_var

The column from phenos that you wish to map to node colour.

size_var

Column to scale node size by.

add_ont_lvl_absolute

Add the absolute ontology level of each HPO term. See get_ontology_levels for more details.

add_ont_lvl_relative

Add the relative ontology level of each HPO term. See get_ontology_levels for more details.

method

Method to construct plot with.

interactive

Make the plot interactive.

verbose

Print messages.

...

Arguments passed on to HPOExplorer::make_network_plot

phenos: A data.table containing HPO IDs and other metadata.
label_var: Column containing the label for each node in a graph (e.g. "hpo_name").
show_plot: Show the plot.
hoverbox_column: Name of the new hoverbox column to add.
preferred_palettes: Preferred palettes to use for each column.

Value

A named list of outputs, including a interactive network plot of the selected subset of results from RD EWCE analysis.

Examples

res <- ggnetwork_plot_full(filters = list(CellType = "Microglia"))
#> ggnetwork_plot_full
#> Subsetting results by q_threshold and effect.
#> Selected CellType : 
#>  - Microglia
#> Filtered 'CellType' : 1,228 / 1,230 rows dropped.
#> 2 associations remain after filtering.
#> 2 associations remain after filtering.
#> Adding HPO names.
#> Translating ontology terms to names.
#> Aggregating results by group_var='hpo_name'/'hpo_id'
#> Warning: argument is not numeric or logical: returning NA
#> Warning: argument is not numeric or logical: returning NA
#> Warning: argument is not numeric or logical: returning NA
#> Warning: argument is not numeric or logical: returning NA
#> Getting absolute ontology level for 19,025 IDs.
#> Getting relative ontology level for 19,025 IDs.
#> Translating ontology terms to ids.
#> Adding term definitions.
#> Adding hoverboxes to data.table.
#> Making phenotype network object.
#> Translating ontology terms to ids.
#> Converted ontology to: tbl_graph 
#> Removing isolated nodes.
#> Loading required namespace: ggnetwork
#> Registered S3 method overwritten by 'ggnetwork':
#>   method         from  
#>   fortify.igraph ggtree
#> Converting graph to ggnetwork.
#> Creating ggnetwork plot.