pathofm_sample_report: Create a single-sample pathology-foundation-model research...

In PathoFMPred: Tumour Feature Models from Pathology Representations

Create a single-sample pathology-foundation-model research output

Description

Create a single-sample pathology-foundation-model research output

Usage

pathofm_sample_report(
  cancer,
  features,
  foundation_model = c("TITAN", "GigaSSL", "ProvGigaPath"),
  patient_id = NULL,
  output_file = NULL,
  format = c("html", "pdf", "both"),
  clinical_context = NULL,
  include_limited_evidence = FALSE,
  quiet = TRUE
)

titan_sample_report(
  cancer,
  features,
  patient_id = NULL,
  output_file = NULL,
  format = c("html", "pdf", "both"),
  clinical_context = NULL,
  include_limited_evidence = FALSE,
  quiet = TRUE
)

Arguments

cancer	A single TCGA cancer code.
features	One or more slide-feature rows for one patient.
foundation_model	One of 'TITAN', 'GigaSSL', or 'ProvGigaPath'.
patient_id	Optional patient/sample identifier for all rows.
output_file	Explicit file stem or '.html'/'.pdf' path. Required; no report is written unless the caller chooses a destination.
format	One of 'html', 'pdf', or 'both'.
clinical_context	Optional named list with 'shared_features', 'pathology', and 'source' character fields. This information is displayed as supplied and is not used by any prediction model.
include_limited_evidence	Explicitly opt in to limited-sample models that still crossed the matched effect threshold for the selected cancer and representation. Tested-below-threshold objects never enter reports.
quiet	Passed to [rmarkdown::render()].

Value

Invisibly, the generated file path(s).

PathoFMPred documentation built on Nov. 12, 2026, 5:10 p.m.