Skip to contents

Heatmap of YLL per 1 000 Admissions by Resistance Class and Pathogen Group

Source: R/prep_daly_plots.R
plot_yll_heatmap.Rd

Produces a tile heatmap where the x-axis shows resistance classes (dominant AMR profiles), the y-axis shows pathogen groups (or individual pathogens), and each cell's fill reflects the associated or attributable YLL burden per 1 000 admissions.

Usage

plot_yll_heatmap(
  data,
  type = c("associated", "attributable"),
  value_col,
  n_admissions = NULL,
  pathogen_col = "pathogen",
  class_col = "profile",
  group_col = NULL,
  syndrome_col = NULL,
  syndrome_name = NULL,
  show_values = TRUE,
  value_digits = 2,
  palette = "Spectral",
  base_size = 14,
  title = NULL,
  subtitle = NULL
)

Arguments

data

Data frame. Must contain the columns named by pathogen_col, class_col, and value_col.

type

Character. "associated" (default) or "attributable". Used only for axis and title labels.

value_col

Character. Required. Column containing the YLL value to plot (e.g. "YLL_class" after distributing per-pathogen YLL across resistance classes, or "YLL_attributable_k" if your data already has one row per pathogen x class).

n_admissions

Numeric or NULL. Total admissions used as the denominator for per-1 000 normalisation. If NULL (default), values are plotted as supplied (assumed pre-normalised).

pathogen_col

Character. Column containing pathogen names. Default "pathogen".

class_col

Character. Column containing the resistance class / dominant profile. Default "profile".

group_col

Character or NULL. Column containing organism group labels (e.g. "org_group"). If NULL (default) or not present in data, pathogen names are used on the y-axis.

syndrome_col

Character or NULL. Syndrome filter column. Default NULL.

syndrome_name

Character or NULL. Syndrome value to retain. Requires syndrome_col. Default NULL.

show_values

Logical. Print rounded values inside each cell. Default TRUE.

value_digits

Integer. Decimal places for cell labels. Default 2.

palette

Character. RColorBrewer palette for the fill scale. Default "Spectral".

base_size

Numeric. Base font size. Default 14.

title

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

subtitle

Character. Custom subtitle. Auto-generated if NULL.

Value

A ggplot object.

Details

The input data should be the $by_class slot (for associated) or the $by_profile slot (for attributable) returned by daly_calc_yll_associated() / daly_calc_yll_attributable(). Both slots contain columns pathogen, profile, and YLL_Kdelta.

If an organism-group column has been pre-joined onto data (e.g. org_group), supply its name via group_col and the function will aggregate to the group x class level. When group_col is NULL or absent, individual pathogen names are used on the y-axis.