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Resistance proportion for top N organisms

Source: R/prep_eda_plots.R
plot_resistance_by_organism.Rd

100 vs Susceptible patients for the top n organisms (ranked by total distinct patient count). A patient × organism pair is classified as Resistant if any antibiotic result for that pair is "R" (worst-phenotype rule at patient × organism × antibiotic level).

Usage

plot_resistance_by_organism(
  data,
  n = 5,
  mode = c("faceted", "overall", "single"),
  center = NULL,
  patient_col = "patient_id",
  organism_col = "organism_normalized",
  antibiotic_col = "antibiotic_name",
  value_col = "result",
  center_col = "center_name",
  colours = NULL,
  base_size = 11,
  ncol = 3,
  title = NULL,
  syndrome_col = NULL,
  syndrome_name = NULL
)

Arguments

data

Data frame (one row per patient × organism × antibiotic result).

n

Number of top organisms to display.

mode

One of "faceted", "overall", or "single".

center

Centre name used when mode = "single".

patient_col

Column for patient ID.

organism_col

Column for organism name.

antibiotic_col

Column for antibiotic name.

value_col

Column for resistance result ("R" / "S").

center_col

Column for centre name.

colours

Named character vector with "R" and "S" entries.

base_size

Base font size for eda_theme().

ncol

Facet columns (faceted mode only).

title

Optional title override.

syndrome_col

Optional column used to pre-filter by syndrome.

syndrome_name

Optional value of syndrome_col to keep.