Validate associations: correlate CellTypeDataset — validate_associations_correlate

Validate phenotype-cell type associations can making comparisons within and between results from different CellTypeDatasets.

validate_associations_correlate_ctd(
  results = load_example_results(),
  filters = NULL,
  hpo_agg_lvl = 3,
  hpo = HPOExplorer::get_hpo(),
  group_var = "ctd",
  celltype_var = "cl_name",
  q_threshold = 0.05,
  downsample = NULL,
  add_density = TRUE,
  marginal = FALSE,
  rasterize_points = TRUE,
  dpi = 100,
  point.args = list(alpha = 0.5),
  stats_idx = c(1, 3, 4, 7),
  ...
)

Arguments

results: The cell type-phenotype enrichment results generated by gen_results and merged together with merge_results
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.
hpo_agg_lvl: Aggregate the data to a specific HPO ancestor level during plotting to reduce figure size.
hpo: Human Phenotype Ontology object, loaded from get_ontology.
group_var: A character string specifying the column in results that contains the group variable to compare across.
celltype_var: A character string specifying the column in results that contains the cell type variable to compare across.
q_threshold: The q value threshold to subset the results by.
downsample: Downsample the data to this many points when plotting.
add_density: Add 2D density plots to the scatter plots.
marginal: Decides whether marginal distributions will be plotted on axes using {ggside} functions. The default is TRUE. The package {ggside} must already be installed by the user.
rasterize_points: Whether to rasterize the points in the scatter plots.
dpi: Resolution of image after rasterization.
point.args: A list of additional aesthetic arguments to be passed to the ggplot2::geom_point().
stats_idx: Indices of statistics to keep in subtitle
...: Additional arguments passed to plot_density_cor.

Examples

results <- load_example_results()[,.SD[seq(10000)],by="ctd"]
#### Across CTD ####
out1 <- validate_associations_correlate_ctd(results=results,
                                            group_var="ctd")
#> Mapping cell types to cell ontology terms.
#> Adding stage information.
#> Adding logFC column.
#> Casting results.
#> 13 comparable celltypes.
#> 62 comparable phenotypes.
#> 3 comparable celltypes @FDR<0.05.
#> 4 comparable phenotypes @FDR<0.05.
#> Generating plots.
#> Force new. Removing existing ancestor columns.
#> Warning: Tried to assign NULL to column 'ancestor', but this column does not exist to remove
#> Warning: Tried to assign NULL to column 'ancestor_name', but this column does not exist to remove
#> Adding level-3 ancestor to each HPO ID.
#> Adding ancestor metadata.
#> Getting absolute ontology level for 18,082 IDs.
#> 344 ancestors found at level 3
#> Translating ontology terms to names.
#> 804 associations remain after filtering.
#> Force new. Removing existing ancestor columns.
#> Warning: Tried to assign NULL to column 'ancestor', but this column does not exist to remove
#> Warning: Tried to assign NULL to column 'ancestor_name', but this column does not exist to remove
#> Adding level-3 ancestor to each HPO ID.
#> Adding ancestor metadata.
#> Getting absolute ontology level for 18,082 IDs.
#> 344 ancestors found at level 3
#> Translating ontology terms to names.
#> 4 associations remain after filtering.
#> Gathering statistics.
#### Within CTD: across developmental stages ####
filters <- list(ctd=c("HumanCellLandscape"), stage=c("Fetus","Adult"))
out2 <- validate_associations_correlate_ctd(results=results,
                                            filters=filters,
                                            group_var="stage")
#> Mapping cell types to cell ontology terms.
#> Adding stage information.
#> Adding logFC column.
#> Filtered 'ctd' : 10,000 / 20,000 rows dropped.
#> Filtered 'stage' : 404 / 10,000 rows dropped.
#> Casting results.
#> 38 comparable celltypes.
#> 81 comparable phenotypes.
#> 9 comparable celltypes @FDR<0.05.
#> 14 comparable phenotypes @FDR<0.05.
#> Generating plots.
#> Force new. Removing existing ancestor columns.
#> Warning: Tried to assign NULL to column 'ancestor', but this column does not exist to remove
#> Warning: Tried to assign NULL to column 'ancestor_name', but this column does not exist to remove
#> Adding level-3 ancestor to each HPO ID.
#> Adding ancestor metadata.
#> Getting absolute ontology level for 18,082 IDs.
#> 344 ancestors found at level 3
#> Translating ontology terms to names.
#> 3,062 associations remain after filtering.
#> Force new. Removing existing ancestor columns.
#> Warning: Tried to assign NULL to column 'ancestor', but this column does not exist to remove
#> Warning: Tried to assign NULL to column 'ancestor_name', but this column does not exist to remove
#> Adding level-3 ancestor to each HPO ID.
#> Adding ancestor metadata.
#> Getting absolute ontology level for 18,082 IDs.
#> 344 ancestors found at level 3
#> Translating ontology terms to names.
#> 17 associations remain after filtering.
#> Gathering statistics.