P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 17:02:03 +02:00
Code Releases Activity

knitr format

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-02-23 16:27:40 +01:00
parent a84101db08
commit e70f2cd32c
10 changed files with 236 additions and 257 deletions
Download Patch File Download Diff File Expand all files Collapse all files

56
R/plot.R
View File

@ -146,18 +146,18 @@ plot.mic <- function(x,
legend_txt <- character(0)
legend_col <- character(0)
if (any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
legend_txt <- "Susceptible"
legend_txt <- c(legend_txt, "(S) Susceptible")
legend_col <- colours_SIR[1]
}
if (any(cols_sub$cols == colours_SIR[2] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, plot_name_of_I(cols_sub$guideline))
legend_txt <- c(legend_txt, paste("(I)", plot_name_of_I(cols_sub$guideline)))
legend_col <- c(legend_col, colours_SIR[2])
}
if (any(cols_sub$cols == colours_SIR[3] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, "Resistant")
legend_txt <- c(legend_txt, "(R) Resistant")
legend_col <- c(legend_col, colours_SIR[3])
}
legend("top",
x.intersp = 0.5,
legend = translate_into_language(legend_txt, language = language),
@ -272,23 +272,25 @@ autoplot.mic <- function(object,
df <- as.data.frame(x, stringsAsFactors = TRUE)
colnames(df) <- c("mic", "count")
df$cols <- cols_sub$cols
df$cols[df$cols == colours_SIR[1]] <- "Susceptible"
df$cols[df$cols == colours_SIR[2]] <- plot_name_of_I(cols_sub$guideline)
df$cols[df$cols == colours_SIR[3]] <- "Resistant"
df$cols[df$cols == colours_SIR[1]] <- "(S) Susceptible"
df$cols[df$cols == colours_SIR[2]] <- paste("(I)", plot_name_of_I(cols_sub$guideline))
df$cols[df$cols == colours_SIR[3]] <- "(R) Resistant"
df$cols <- factor(translate_into_language(df$cols, language = language),
levels = translate_into_language(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
language = language
),
ordered = TRUE
levels = translate_into_language(c("(S) Susceptible",
paste("(I)", plot_name_of_I(cols_sub$guideline)),
"(R) Resistant"),
language = language
),
ordered = TRUE
)
p <- ggplot2::ggplot(df)
if (any(colours_SIR %in% cols_sub$cols)) {
vals <- c(
"Susceptible" = colours_SIR[1],
"Susceptible, incr. exp." = colours_SIR[2],
"Intermediate" = colours_SIR[2],
"Resistant" = colours_SIR[3]
"(S) Susceptible" = colours_SIR[1],
"(I) Susceptible, incr. exp." = colours_SIR[2],
"(I) Intermediate" = colours_SIR[2],
"(R) Resistant" = colours_SIR[3]
)
names(vals) <- translate_into_language(names(vals), language = language)
p <- p +
@ -386,15 +388,15 @@ plot.disk <- function(x,
legend_txt <- character(0)
legend_col <- character(0)
if (any(cols_sub$cols == colours_SIR[3] & cols_sub$count > 0)) {
legend_txt <- "Resistant"
legend_txt <- "(R) Resistant"
legend_col <- colours_SIR[3]
}
if (any(cols_sub$cols == colours_SIR[2] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, plot_name_of_I(cols_sub$guideline))
legend_txt <- c(legend_txt, paste("(I)", plot_name_of_I(cols_sub$guideline)))
legend_col <- c(legend_col, colours_SIR[2])
}
if (any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, "Susceptible")
legend_txt <- c(legend_txt, "(S) Susceptible")
legend_col <- c(legend_col, colours_SIR[1])
}
legend("top",
@ -512,11 +514,13 @@ autoplot.disk <- function(object,
colnames(df) <- c("disk", "count")
df$cols <- cols_sub$cols
df$cols[df$cols == colours_SIR[1]] <- "Susceptible"
df$cols[df$cols == colours_SIR[2]] <- plot_name_of_I(cols_sub$guideline)
df$cols[df$cols == colours_SIR[3]] <- "Resistant"
df$cols[df$cols == colours_SIR[1]] <- "(S) Susceptible"
df$cols[df$cols == colours_SIR[2]] <- paste("(I)", plot_name_of_I(cols_sub$guideline))
df$cols[df$cols == colours_SIR[3]] <- "(R) Resistant"
df$cols <- factor(translate_into_language(df$cols, language = language),
levels = translate_into_language(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
levels = translate_into_language(c("(S) Susceptible",
paste("(I)", plot_name_of_I(cols_sub$guideline)),
"(R) Resistant"),
language = language
),
ordered = TRUE
@ -525,10 +529,10 @@ autoplot.disk <- function(object,
if (any(colours_SIR %in% cols_sub$cols)) {
vals <- c(
"Susceptible" = colours_SIR[1],
"Susceptible, incr. exp." = colours_SIR[2],
"Intermediate" = colours_SIR[2],
"Resistant" = colours_SIR[3]
"(S) Susceptible" = colours_SIR[1],
"(I) Susceptible, incr. exp." = colours_SIR[2],
"(I) Intermediate" = colours_SIR[2],
"(R) Resistant" = colours_SIR[3]
)
names(vals) <- translate_into_language(names(vals), language = language)
p <- p +