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Plot cytogenetic oncoprint

Source: R/08_cytogenetic_viz.R
plot_cytogenetic_oncoprint.Rd

Creates an oncoprint-style heatmap showing cytogenetic alterations across patients. Rows are alterations, columns are patients. Uses ggplot2 for portability (no ComplexHeatmap dependency).

Usage

plot_cytogenetic_oncoprint(
  cyto_data,
  markers = NULL,
  sort_by = c("frequency", "risk"),
  title = "Cytogenetic Landscape"
)

Arguments

cyto_data

Data frame from extract_cytogenetic_data() with columns: patient_id, iss_stage, t_4_14, t_11_14, t_14_16, del_17p, gain_1q, etc.

markers

Character vector of marker columns to include. Default uses all available markers.

sort_by

How to sort patients. One of "frequency" (default) or "risk".

title

Plot title.

Value

A ggplot object

See also

Other cytogenetics: calculate_cooccurrence(), compute_riss(), extract_cytogenetic_data(), plot_cooccurrence_heatmap(), plot_expression_by_subtype(), summarize_cytogenetics()

Examples

if (FALSE) { # \dontrun{
cyto <- arrow::read_parquet("data/raw/clinical/cytogenetic_data.parquet")
plot_cytogenetic_oncoprint(cyto)
} # }