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(v3.0.0.9015) plotting fix

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2025-07-19 14:06:36 +02:00
parent 49274f010b
commit 6cb724a208
5 changed files with 6 additions and 6 deletions
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DESCRIPTION
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@@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 3.0.0.9014 Version: 3.0.0.9015
Date: 2025-07-18 Date: 2025-07-19
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by
NEWS.md
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# AMR 3.0.0.9014 # AMR 3.0.0.9015
This is primarily a bugfix release, though we added one nice feature too. This is primarily a bugfix release, though we added one nice feature too.
R/ggplot_sir.R
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@@ -177,8 +177,8 @@ ggplot_sir <- function(data,
nrow = NULL, nrow = NULL,
colours = c( colours = c(
S = "#3CAEA3", S = "#3CAEA3",
SI = "#3CAEA3",
SDD = "#8FD6C4", SDD = "#8FD6C4",
SI = "#3CAEA3",
I = "#F6D55C", I = "#F6D55C",
IR = "#ED553B", IR = "#ED553B",
R = "#ED553B" R = "#ED553B"
R/plotting.R
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@@ -1490,7 +1490,7 @@ labels_sir_count <- function(position = NULL,
} }
expand_SIR_colours <- function(colours_SIR, unname = TRUE) { expand_SIR_colours <- function(colours_SIR, unname = TRUE) {
sir_order <- c("S", "SDD", "I", "R") sir_order <- c("S", "SDD", "SI", "I", "IR", "R")
if (is.null(names(colours_SIR))) { if (is.null(names(colours_SIR))) {
if (length(colours_SIR) == 1) { if (length(colours_SIR) == 1) {
man/ggplot_sir.Rd
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@@ -9,7 +9,7 @@ ggplot_sir(data, position = NULL, x = "antibiotic",
fill = "interpretation", facet = NULL, breaks = seq(0, 1, 0.1), fill = "interpretation", facet = NULL, breaks = seq(0, 1, 0.1),
limits = NULL, translate_ab = "name", combine_SI = TRUE, limits = NULL, translate_ab = "name", combine_SI = TRUE,
minimum = 30, language = get_AMR_locale(), nrow = NULL, colours = c(S minimum = 30, language = get_AMR_locale(), nrow = NULL, colours = c(S
= "#3CAEA3", SI = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", IR = "#ED553B", = "#3CAEA3", SDD = "#8FD6C4", SI = "#3CAEA3", I = "#F6D55C", IR = "#ED553B",
R = "#ED553B"), datalabels = TRUE, datalabels.size = 2.5, R = "#ED553B"), datalabels = TRUE, datalabels.size = 2.5,
datalabels.colour = "grey15", title = NULL, subtitle = NULL, datalabels.colour = "grey15", title = NULL, subtitle = NULL,
caption = NULL, x.title = "Antimicrobial", y.title = "Proportion", ...) caption = NULL, x.title = "Antimicrobial", y.title = "Proportion", ...)