Package index • zhncommandR

Launch the dashboard

zhn_run_app(): Launch the zhncommandR Shiny dashboard
zhn_example_path(): Path to the bundled synthetic example workbook

Readers

Read tumour-documentation Excel sheets.

zhn_read_cohort() experimental: Read the cohort sheet (Basisdaten / Faelle)
zhn_read_therapy(): Read the OPS-8-544 (complex chemotherapy) sheet
zhn_read_diagnostics(): Read the OPS-1-941 (complex diagnostics) sheet
zhn_read_tumorboard(): Read previously exported tumour-board decisions

Parsers

Reshape and classify the raw sheets for downstream analysis.

zhn_prepare_therapy_blocks() experimental: Prepare OPS-8-544 therapy blocks for downstream analysis
zhn_prepare_diagnostic_blocks() experimental: Prepare OPS-1-941 complex-diagnostics blocks
zhn_parse_oncoprint() experimental: Parse the oncoprint free-text mutation column
zhn_parse_cytogenetics() experimental: Parse the cytogenetics free-text column

Alteration classification helpers

zhn_normalize_alteration(): Normalise a free-text alteration label
zhn_alteration_type(): Classify a free-text alteration string
zhn_is_mutation(): Logical: should this alteration class appear in the oncoprint?

S3 classes

Constructors for the data-frame wrappers returned by readers and parsers.

new_cohort_df(): Cohort data frame
new_therapy_blocks(): Therapy-blocks data frame
new_diagnostic_blocks(): Diagnostic-blocks data frame

Figures

Publication-ready figures in the Hugo Coder look.

zhn_plot_diagnoses(): Figure: top diagnoses / codings (horizontal bar)
zhn_plot_cases_by_year(): Figure: cases per treatment year (vertical bar)
zhn_plot_km(): Publication-ready Kaplan-Meier plot (ggsurvfit)
zhn_km_pairwise(): Pairwise log-rank comparisons with Benjamini-Hochberg correction
zhn_theme(): zhncommandR figure theme (Hugo Coder look)
zhn_pal: zhncommandR figure palette

Export and fonts

Save figures to paper-ready files and register the bundled font.

zhn_save_plot(): Save a zhncommandR figure to PNG (600 dpi) or PDF (vector)
zhn_register_fonts(): Register the bundled Inter font for live display and exports