Skip to contents

Plot Top Pathogens by Unique Patients

Source: R/prep_eda_plots.R
plot_top_organisms.Rd

Produces a horizontal bar chart of the top n organisms ranked by unique patient count. Supports three display modes:

  • "faceted" – one panel per centre, top n organisms within each centre independently. Facet strips show patient and organism counts for that centre.

  • "overall" – all centres pooled; single chart of the top n organisms across the entire dataset.

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

Usage

plot_top_organisms(
  data,
  n = 5,
  mode = c("faceted", "overall", "single"),
  center = NULL,
  patient_col = "PatientInformation_id",
  organism_col = "organism_name",
  center_col = "center_name",
  fill_colour = "steelblue",
  ncol = 2,
  base_size = 14,
  title = NULL,
  syndrome_col = NULL,
  syndrome_name = NULL
)

Arguments

data

Data frame. Long-format AMR dataset (one row per isolate/antibiotic record).

n

Integer. Number of top organisms to show. 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 (must match a value in center_col).

patient_col

Character. Column name for patient identifiers. Default "PatientInformation_id".

organism_col

Character. Column name for organism names. Default "organism_name".

center_col

Character. Column name for centre/facility names. Default "center_name".

fill_colour

Character. Bar fill colour (any R colour string or hex). Default "steelblue".

ncol

Integer. Number of columns in the facet grid (mode = "faceted" only). Default 2.

base_size

Numeric. Base font size passed to eda_theme(). Default 14.

title

Character. Custom plot title. If NULL a title is generated automatically from mode and n. 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. Print it or pass to ggsave().

Details

Labels on each bar show absolute count and percentage of that centre's (or overall) unique patient total.