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Heatmap of YLD per 1 000 Admissions by Organism Group

Source: R/prep_daly_plots.R
plot_yld_heatmap.Rd

Produces a two-column tile heatmap where the x-axis shows YLD Associated and YLD Attributable, the y-axis shows organism groups (or individual pathogens), and each cell's fill reflects the YLD burden per 1 000 admissions.

Usage

plot_yld_heatmap(
  data,
  n_admissions = NULL,
  pathogen_col = "pathogen",
  assoc_col = "YLD_associated",
  attr_col = "YLD_attributable",
  group_col = NULL,
  syndrome_col = NULL,
  syndrome_name = NULL,
  show_values = TRUE,
  value_digits = 2,
  palette = "Blues",
  coord_fixed = TRUE,
  base_size = 14,
  title = NULL,
  subtitle = NULL
)

Arguments

data

Data frame. Must contain the columns named by pathogen_col, assoc_col, and attr_col.

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".

assoc_col

Character. Column containing YLD associated values. Default "YLD_associated".

attr_col

Character. Column containing YLD attributable values. Default "YLD_attributable".

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 "Blues".

coord_fixed

Logical. Whether to apply ggplot2::coord_fixed() to produce square tiles. Default TRUE.

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 contain one row per pathogen with YLD_associated and YLD_attributable columns – typically the output of daly_calc_yld_attributable() (which augments the data frame with both columns). If an organism-group column has been pre-joined (e.g. org_group), supply its name via group_col to aggregate cells to the group level.