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Create an Upset plot for AMR data

Source: R/amr_complexUpset.R
amr_complexUpset.Rd

This function generates an Upset plot using a binary matrix of genetic determinants and antimicrobial resistance (AMR) data. Optionally, MIC or disk diffusion breakpoints can be overlaid on the plot.

Usage

amr_complexUpset(
  binary_matrix,
  min_set_size = 10,
  mic_disk = "mic",
  remove_NAs = TRUE,
  gene_determinants = NULL,
  colour_by = "pheno",
  plot_breakpoints = FALSE,
  organism = NULL,
  break_guide = "EUCAST 2024",
  break_type = "ECOFF",
  drug = NULL,
  sort_intersections_by = "degree",
  sort_intersections = "ascending",
  show_intersect_size = TRUE,
  intersect_counts = TRUE,
  heights = NULL,
  colour_values = c(S = "#66c2a5", I = "#fdae61", R = "#d53e4f")
)

Arguments

binary_matrix

A binary matrix where rows represent samples and columns represent genetic determinants or phenotypic resistance data.

min_set_size

The minimum size of a set to be included in the plot. Default is 10.

mic_disk

A character string specifying whether to use 'mic' or 'disk' for the y-axis. Must be either "mic" or "disk". Default is "mic".

remove_NAs

Logical. If TRUE, removes rows with missing values in the selected mic_disk column. Default is TRUE.

gene_determinants

A character vector specifying which genetic determinants to include. If NULL, all genes are used. Default is NULL.

colour_by

A character string specifying the column used for colour mapping in the plot. Default is "pheno".

plot_breakpoints

Logical. If TRUE, overlays MIC or disk diffusion breakpoints on the plot. Default is FALSE.

organism

A character string specifying the organism, used when plotting breakpoints.

break_guide

A character string specifying the breakpoint guideline (e.g., "EUCAST 2024"). Default is "EUCAST 2024".

break_type

A character string specifying the breakpoint type (e.g., "ECOFF"). Default is "ECOFF".

drug

A character string specifying the antimicrobial agent to be analysed.

colour_values

A named vector specifying colours for different resistance categories (S, I, R). Default is c(S="#66c2a5", I="#fdae61", R="#d53e4f").

Value

A ggplot object displaying the Upset plot.

Examples

# Example usage:

ecoli_geno <- import_amrfp(ecoli_geno_raw, "Name")
#> Input is already a dataframe.

binary_matrix<- get_binary_matrix(geno_table=ecoli_geno, 
              pheno_table=ecoli_ast, 
              antibiotic="Ciprofloxacin", 
              drug_class_list=c("Quinolones"), 
              sir_col="pheno", 
              keep_assay_values=TRUE, 
              keep_assay_values_from = "mic"
           )
#> [1] "Some samples had multiple phenotype rows, taking the most resistant only"
#> [1] "Defining NWT using ecoff column provided: ecoff"

amr_complexUpset(binary_matrix)
#> Warning: Removed 171 rows containing non-finite outside the scale range (`stat_sum()`).