Plot bar dendrogram

Source: R/plot_bar_dendro.R

Create a plot summarising MSTExplorer results as a bar chart with multiple facets showing selected branches from the Human Phenotype Ontology (HPO). Also shows a dendrogram of celltype-celltype relationships using the Cell Ontology (CL).

plot_bar_dendro(
  results = load_example_results(),
  celltype_col = "cl_name",
  target_branches = get_target_branches(),
  keep_ancestors = names(target_branches),
  hpo = HPOExplorer::get_hpo(),
  cl = KGExplorer::get_ontology(name = "cl", lvl = 1, remove_rings = TRUE),
  facets = "ancestor_name",
  add_test_target_celltypes = TRUE,
  preferred_palettes = "tol",
  legend.position = "none",
  heights = c(0.3, 1, 0.15, 0.3),
  expand_dendro_x = rep(0.01, 2),
  q_threshold = 0.05,
  show_plot = TRUE,
  save_path = NULL,
  height = 16,
  width = 13,
  ...
)

Arguments

results

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

celltype_col

Name of the cell type column in the results.

target_branches

A named list of HPO branches each matched with CL cell type branches that correspond to on-target cell types across the two ontologies.

keep_ancestors

Only HPO terms that have these ancestors will be kept.

hpo

Human Phenotype Ontology object, loaded from get_ontology.

cl

Cell Ontology (CL) object from KGExplorer::get_ontology("cl").

facets

A set of variables or expressions quoted by vars() and defining faceting groups on the rows or columns dimension. The variables can be named (the names are passed to labeller).

For compatibility with the classic interface, can also be a formula or character vector. Use either a one sided formula, ~a + b, or a character vector, c("a", "b").

add_test_target_celltypes

Using the significant phenotype-cell type association results, run proportional enrichment tests to determine whether each cell type is overrepresented in a given HPO branch relative to all other HPO branches. Overrepresented cell types will be denoted by "*" above its bar.

preferred_palettes

Preferred palettes to use for each column.

legend.position

the default position of legends ("none", "left", "right", "bottom", "top", "inside")

heights

Passed to wrap_plots.

expand_dendro_x

Passed to scale_x_discrete in the cell type dendrogram.

q_threshold

The q value threshold to subset the results by.

show_plot

Print the plot to the console.

save_path

Save the plot to a file. Set to NULL to not save the plot.

height

Height of the saved plot.

width

Width of the saved plot.

...

Arguments passed on to EWCE::ewce_plot

total_res

Results data.frame generated using bootstrap_enrichment_test or ewce_expression_data functions. Multiple results tables can be merged into one results table, as long as the 'list' column is set to distinguish them. Multiple testing correction is then applied across all merged results.

mtc_method

Method to be used for multiple testing correction. Argument is passed to p.adjust (DEFAULT: "bonferroni).

ctd

CellTypeDataset object. Should be provided so that the dendrogram can be taken from it and added to plots.

annotLevel

An integer indicating which level of ctd to analyse (Default: 1).

make_dendro

Add a dendrogram (requires ctd).

verbose

Print messages.

Value

A bar chart with dendrogram of EWCE results in each cell type.

Examples

results <- load_example_results()
out <- plot_bar_dendro(results = results)
#> Loading required namespace: ggdendro
#> Adding HPO names.
#> Translating ontology terms to names.
#> Adding level-2 ancestor to each HPO ID.
#> Adding ancestor metadata.
#> Ancestor metadata already present. Use force_new=TRUE to overwrite.
#> 2,201,892 associations remain after filtering.
#> Mapping cell types to cell ontology terms.
#> Adding stage information.
#> Filtered 'ancestor_name' : 997,803 / 2,201,892 rows dropped.
#> Translating ontology terms to ids.
#> Loading cached ontology: /github/home/.cache/R/KGExplorer/cl.rds
#> Translating ontology terms to ids.
#> Translating ontology terms to ids.
#> Translating ontology terms to ids.
#> Translating ontology terms to ids.
#> Translating ontology terms to ids.
#> Translating ontology terms to ids.
#> Loading cached ontology: /github/home/.cache/R/KGExplorer/cl.rds
#> Translating ontology terms to ids.
#> Translating ontology terms to ids.
#> Converted ontology to: igraph 
#> Converted ontology to: igraph_dist 
#> Translating ontology terms to names.
#> Adding logFC column.
#> Using palette: tol
#> Cell type columns already present. Skipping mapping.
#> Ancestor columns already present. Skipping.
#> 2,201,892 associations remain after filtering.
#> Cell type columns already present. Skipping mapping.
#> Running tests: across_branches_per_celltype
#> Warning: Invalid .internal.selfref detected and fixed by taking a (shallow) copy of the data.table so that := can add this new column by reference. At an earlier point, this data.table has been copied by R (or was created manually using structure() or similar). Avoid names<- and attr<- which in R currently (and oddly) may copy the whole data.table. Use set* syntax instead to avoid copying: ?set, ?setnames and ?setattr. If this message doesn't help, please report your use case to the data.table issue tracker so the root cause can be fixed or this message improved.
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.
#> Ancestor columns already present. Skipping.
#> 2,201,892 associations remain after filtering.
#> Cell type columns already present. Skipping mapping.
#> Translating ontology terms to ids.
#> Loading cached ontology: /github/home/.cache/R/KGExplorer/cl.rds
#> Translating ontology terms to ids.
#> Translating ontology terms to ids.
#> Translating ontology terms to ids.
#> Translating ontology terms to ids.
#> Translating ontology terms to ids.
#> Translating ontology terms to ids.
#> Proportional enrichment summary stats:
#>  - pct_min: 17.2
#>  - pct_max: 64.93
#>  - pct_max_mean: 39.95
#>  - pct_max_sd: 17.7
#>  - enrichment_mean: 4.75