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Plot Final Outcome Proportions for Resistant or Susceptible Patients

Source: R/prep_eda_plots.R
plot_outcome_by_organism.Rd

Produces a 100% horizontal stacked bar chart showing the distribution of final outcomes (Death, Discharged, LAMA, Referred) for the top n organisms, split by whether the patient had a Resistant or Susceptible result.

Usage

plot_outcome_by_organism(
  data,
  n = 5,
  resistance_filter = c("R", "S"),
  mode = c("faceted", "overall", "single"),
  center = NULL,
  patient_col = "PatientInformation_id",
  organism_col = "organism_name",
  antibiotic_col = "antibiotic_name",
  value_col = "antibiotic_value",
  outcome_col = "final_outcome",
  center_col = "center_name",
  merge_referred = TRUE,
  palette = c(Death = "#E74C3C", Died = "#E74C3C", Discharged = "#2ECC71", LAMA =
    "#95A5A6", Referred = "#3498DB", `Transferred to other hospital` = "#3498DB"),
  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 organisms to show. Default 5.

resistance_filter

Character. "R" or "S". Which patient group to display. Default "R".

mode

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

center

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

patient_col

Character. Patient ID column. Default "PatientInformation_id".

organism_col

Character. Organism name column. Default "organism_name".

antibiotic_col

Character. Antibiotic name column. Default "antibiotic_name".

value_col

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

outcome_col

Character. Final outcome column. Default "final_outcome".

center_col

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

merge_referred

Logical. Recode "Transferred to other hospital" to "Referred". Default TRUE.

palette

Named character vector mapping outcome values to colours. Unmatched outcomes get grey automatically.

ncol

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

base_size

Numeric. Base font size. Default 14.

title

Character. Custom 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. If NULL (default), all syndromes are included.

Value

A ggplot object.

Details

Each bar represents one organism. The fill shows outcome proportions. A n= label is printed above each bar showing the total number of unique patients in that organism x resistance group.

Resistance grouping: resistance_filter = "R" shows patients who had at least one R result for the given organism. "S" shows patients with only S results. Because these groups overlap (a patient resistant to one antibiotic may be susceptible to another), calling the function twice – once for "R" and once for "S" – gives the most complete picture.

Top N organisms are ranked by total unique patients per centre (or globally for mode = "overall"), calculated before the R/S split so the same organisms appear in both R and S plots.

Supports three display modes:

  • "faceted" (default) – one panel per centre.

  • "overall" – all centres pooled.

  • "single" – one specific centre.