Predict cell types

Source: R/predict_celltypes.R

Predict the causal cell types underlying a patient's phenotypes given some varying degree of prior knowledge.

predict_celltypes(
  phenotypes,
  diseases_include = NULL,
  diseases_exclude = NULL,
  genes_include = NULL,
  genes_exclude = NULL,
  gene_weights = list(include = 2, default = 1, exclude = 0),
  results = MSTExplorer::load_example_results(),
  phenotype_to_genes = HPOExplorer::load_phenotype_to_genes(),
  agg_var = c("cl_name"),
  effect_var = "logFC",
  x_var = agg_var[1],
  y_var = "score_mean",
  fill_var = "score_sum",
  evidence_score_var = "evidence_score_sum",
  max_x_var = 10,
  subtitle_size = 9,
  plot.margin = ggplot2::margin(1, 1, 1, 40),
  show_plot = TRUE,
  save_path = NULL,
  width = NULL,
  height = NULL
)

Arguments

phenotypes

Phenotypes observed in the patient. Can be a list of HPO phenotype IDs or HPO phenotype names.

diseases_include

Diseases that the patient is known to have. Can be provided as OMIM, Orphanet, or DECIPHER disease IDs.

diseases_exclude

Diseases that the patient is known NOT to have. Can be provided as OMIM, Orphanet, or DECIPHER disease IDs.

genes_include

Genes in which the patient is known to have abnormalities.

genes_exclude

Genes in which the patient is known NOT to have abnormalities.

gene_weights

A named list describing the weight to apply to genes in the include, default, and exclude lists.

results

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

phenotype_to_genes

Phenotype to gene mapping from load_phenotype_to_genes.

agg_var

The variable(s) to aggregate results by.

effect_var

Name of the effect size column in the results.

x_var

Variable to plot on the x-axis.

y_var

Variable to plot on the y-axis.

fill_var

Variable to fill by.

evidence_score_var

Which variable from add_evidence to use when weighting genes.

max_x_var

The maximum number of cell types to display.

subtitle_size

Size of the plot subtitle.

plot.margin

margin around entire plot (unit with the sizes of the top, right, bottom, and left margins)

show_plot

Print the plot to the console.

save_path

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

width

Width of the saved plot.

height

Height of the saved plot.

Value

data.table of prioritised cell types, sorted by a "score" that combines:

  • The phenotype-cell type enrichment p-values ("p").

  • The phenotype-cell type enrichment effect size ("effect").

  • A gene-wise factor that upweights/downweights included/excluded genes respectively, multiplied by the evidence score of a phenotype-gene association. Only applied when genes_include or genes_exclude is provided.

Examples

phenotypes <- c("Generalized neonatal hypotonia",
                "Scrotal hypospadias",
                "Increased circulating progesterone")
# diseases_include <- "OMIM:176270"
genes_include <- c("MAGEL2","HERC2")
genes_exclude <- c("SNORD115-1")
ct <- predict_celltypes(phenotypes = phenotypes,
                        genes_include = genes_include,
                        genes_exclude = genes_exclude)
#> Translating ontology terms to ids.
#> Adding logFC column.
#> Reading cached RDS file: phenotype_to_genes.txt
#> + Version: v2024-12-12
#> Adding genes and disease IDs.
#> Mapping cell types to cell ontology terms.
#> Adding stage information.
#> Reading cached RDS file: phenotype_to_genes.txt
#> + Version: v2024-12-12
#> Loading ctd_DescartesHuman.rds
#> Loading ctd_HumanCellLandscape.rds
#> Annotating gene-disease associations with Evidence Score
#> Gathering data from GenCC.
#> Importing cached file.
#> Evidence scores for: 
#>  - 10514 diseases 
#>  - 5171 genes
#> + Version: 2024-12-19
#> 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.