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(v1.5.0.9032) All group generics for MICs

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dr. M.S. (Matthijs) Berends
2021-03-07 13:52:39 +01:00
parent 91dd755cac
commit 850c123de7
40 changed files with 641 additions and 203 deletions
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21
R/plot.R
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@ -108,7 +108,6 @@ plot.mic <- function(x,
fn = as.mic,
language = language,
...)
barplot(x,
col = cols_sub$cols,
main = main,
@ -116,7 +115,7 @@ plot.mic <- function(x,
ylab = ylab,
xlab = xlab,
axes = FALSE)
axis(2, seq(0, max(as.double(x))))
axis(2, seq(0, max(x)))
if (!is.null(cols_sub$sub)) {
mtext(side = 3, line = 0.5, adj = 0.5, cex = 0.75, cols_sub$sub)
}
@ -124,15 +123,15 @@ plot.mic <- function(x,
if (any(colours_RSI %in% cols_sub$cols)) {
legend_txt <- character(0)
legend_col <- character(0)
if (colours_RSI[2] %in% cols_sub$cols) {
if (any(cols_sub$cols == colours_RSI[2] & cols_sub$count > 0)) {
legend_txt <- "Susceptible"
legend_col <- colours_RSI[2]
}
if (colours_RSI[3] %in% cols_sub$cols) {
if (any(cols_sub$cols == colours_RSI[3] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, plot_name_of_I(cols_sub$guideline))
legend_col <- c(legend_col, colours_RSI[3])
}
if (colours_RSI[1] %in% cols_sub$cols) {
if (any(cols_sub$cols == colours_RSI[1] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, "Resistant")
legend_col <- c(legend_col, colours_RSI[1])
}
@ -317,15 +316,15 @@ plot.disk <- function(x,
if (any(colours_RSI %in% cols_sub$cols)) {
legend_txt <- character(0)
legend_col <- character(0)
if (colours_RSI[1] %in% cols_sub$cols) {
if (any(cols_sub$cols == colours_RSI[1] & cols_sub$count > 0)) {
legend_txt <- "Resistant"
legend_col <- colours_RSI[1]
}
if (colours_RSI[3] %in% cols_sub$cols) {
if (any(cols_sub$cols == colours_RSI[3] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, plot_name_of_I(cols_sub$guideline))
legend_col <- c(legend_col, colours_RSI[3])
}
if (colours_RSI[2] %in% cols_sub$cols) {
if (any(cols_sub$cols == colours_RSI[2] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, "Susceptible")
legend_col <- c(legend_col, colours_RSI[2])
}
@ -459,8 +458,8 @@ plot_prepare_table <- function(x, expand) {
if (is.mic(x)) {
if (expand == TRUE) {
# expand range for MIC by adding factors of 2 from lowest to highest so all MICs in between also print
extra_range <- max(as.double(x)) / 2
while (min(extra_range) / 2 > min(as.double(x))) {
extra_range <- max(x) / 2
while (min(extra_range) / 2 > min(x)) {
extra_range <- c(min(extra_range) / 2, extra_range)
}
nms <- extra_range
@ -525,7 +524,7 @@ plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_RSI, f
cols <- "#BEBEBE"
sub <- NULL
}
list(cols = cols, sub = sub, guideline = guideline)
list(cols = cols, count = as.double(x), sub = sub, guideline = guideline)
}