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Plot Antibiotic Susceptibility Pattern (Stacked R/S Bars)

Source: R/prep_eda_plots.R
plot_abx_susceptibility.Rd

Produces a horizontal stacked bar chart showing the number of admissions tested as Resistant (R) or Susceptible (S) for the top n antibiotics. Percentage labels are shown inside each bar segment.

Usage

plot_abx_susceptibility(
  data,
  n = 5,
  mode = c("faceted", "overall", "single"),
  center = NULL,
  patient_col = "PatientInformation_id",
  antibiotic_col = "antibiotic_name",
  value_col = "antibiotic_value",
  organism_col = "organism_name",
  center_col = "center_name",
  colours = c(R = "#D73027", S = "#1A9850"),
  ncol = 2,
  base_size = 14,
  title = NULL,
  syndrome_col = NULL,
  syndrome_name = NULL
)

Arguments

data

Data frame. Long-format AMR dataset.

n

Integer. Number of top antibiotics to show (ranked by total patients tested). Default 5.

mode

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

center

Character. Required when mode = "single". Exact name of the centre to plot.

patient_col

Character. Patient ID column. Default "PatientInformation_id".

antibiotic_col

Character. Antibiotic name column. Default "antibiotic_name".

value_col

Character. Susceptibility result column containing "R" and "S" values. Default "antibiotic_value".

organism_col

Character. Organism name column (used in worst-phenotype deduplication). Default "organism_name".

center_col

Character. Centre/facility column. Default "center_name".

colours

Named character vector. Fill colours for R and S. Default c("R" = "#D73027", "S" = "#1A9850").

ncol

Integer. Facet columns (mode = "faceted" only). Default 2.

base_size

Numeric. Base font size. Default 14.

title

Character. Custom plot title. Auto-generated if NULL. Default NULL.

syndrome_col

Character or NULL. Column name containing syndrome/infection category labels (e.g. "infectious_syndrome"). If NULL (default), no syndrome filtering is applied.

syndrome_name

Character or NULL. The syndrome value to retain (e.g. "BSI", "VAP"). Requires syndrome_col to be set. If NULL (default), all syndromes are included.

Value

A ggplot object.

Details

Worst-phenotype rule: when a patient has multiple records for the same organism-antibiotic combination, any single R result marks the whole episode as R. This prevents double-counting repeat cultures from the same infection episode.

Counting unit: bars show unique patients (not isolate rows), so a patient tested against the same antibiotic twice is counted once.

Supports three display modes:

  • "faceted" – top n antibiotics per centre independently, one panel per centre.

  • "overall" – all centres pooled; top n antibiotics globally.

  • "single" – one specific centre; pass the centre name via center.