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Plot Antibiotic Resistance Heatmap

Source: R/prep_eda_plots.R
plot_abx_heatmap.Rd

Produces a ggplot2 tile heatmap where:

  • x-axis – antibiotics (ordered by total patients tested, most tested on the left)

  • y-axis – centres

  • fill colour – proportion of patients who were Resistant for that antibiotic at that centre (0 = fully susceptible, 1 = fully resistant)

Usage

plot_abx_heatmap(
  data,
  n = NULL,
  mode = c("all", "single"),
  center = NULL,
  patient_col = "PatientInformation_id",
  antibiotic_col = "antibiotic_name",
  value_col = "antibiotic_value",
  organism_col = "organism_name",
  center_col = "center_name",
  show_values = TRUE,
  midpoint = 0.5,
  low_colour = "#1a9850",
  mid_colour = "#fee08b",
  high_colour = "#d73027",
  base_size = 14,
  title = NULL,
  syndrome_col = NULL,
  syndrome_name = NULL
)

Arguments

data

Data frame. Long-format AMR dataset.

n

Integer or NULL. If an integer, only the top n antibiotics by total patients tested are shown. If NULL, all antibiotics are shown. Default NULL.

mode

Character. "all" or "single". Default "all".

center

Character. Required when mode = "single". Exact centre name.

patient_col

Character. Patient ID column. Default "PatientInformation_id".

antibiotic_col

Character. Antibiotic name column. Default "antibiotic_name".

value_col

Character. Susceptibility result column (R/S values). Default "antibiotic_value".

organism_col

Character. Organism name column. Default "organism_name".

center_col

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

show_values

Logical. Print proportion values inside tiles. Default TRUE.

midpoint

Numeric. Midpoint of the colour gradient (0-1). Default 0.5.

low_colour

Character. Colour for proportion = 0 (fully susceptible). Default "#1a9850" (green).

mid_colour

Character. Colour for the midpoint. Default "#fee08b" (yellow).

high_colour

Character. Colour for proportion = 1 (fully resistant). Default "#d73027" (red).

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

Only R and S results are used. The same worst-phenotype rule as plot_abx_susceptibility() is applied: per patient x organism x antibiotic, any single R marks the episode as R.

Cells with no data (antibiotic not tested at that centre) are shown in light grey.

Supports two display modes:

  • "all" (default) – all centres on the y-axis.

  • "single" – filter to one centre before plotting (produces a single-row heatmap useful for per-centre reports).