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(v0.6.1.9046) ggplot fix

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dr. M.S. (Matthijs) Berends 2019-05-31 20:25:57 +02:00
parent f03f71eced
commit 4ed27c7e7a
15 changed files with 287 additions and 191 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 0.6.1.9045 Version: 0.6.1.9046
Date: 2019-05-31 Date: 2019-05-31
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

4
NEWS.md
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@ -22,6 +22,9 @@
system.file("translations.tsv", package = "AMR") system.file("translations.tsv", package = "AMR")
``` ```
Please create an issue in one of our repositories if you want additions in this file. Please create an issue in one of our repositories if you want additions in this file.
* Improvements to plotting AMR results with `ggplot_rsi()`:
* New parameter `colours` to set the bar colours
* New parameters `title`, `subtitle`, `caption`, `x.title` and `y.title` to set titles and axis descriptions
* Improved intelligence of looking up antibiotic tables in data set using `guess_ab_col()` * Improved intelligence of looking up antibiotic tables in data set using `guess_ab_col()`
* Added ~5,000 more old taxonomic names to the `microorganisms.old` data set, which leads to better results finding when using the `as.mo()` function * Added ~5,000 more old taxonomic names to the `microorganisms.old` data set, which leads to better results finding when using the `as.mo()` function
* This package now honours the new EUCAST insight (2019) that S and I are but classified as susceptible, where I is defined as 'increased exposure' and not 'intermediate' anymore. For functions like `portion_df()` and `count_df()` this means that their new parameter `combine_SI` is TRUE at default. * This package now honours the new EUCAST insight (2019) that S and I are but classified as susceptible, where I is defined as 'increased exposure' and not 'intermediate' anymore. For functions like `portion_df()` and `count_df()` this means that their new parameter `combine_SI` is TRUE at default.
@ -50,6 +53,7 @@
* Function `as.mo()` now gently interprets any number of whitespace characters (like tabs) as one space * Function `as.mo()` now gently interprets any number of whitespace characters (like tabs) as one space
* Small algorithm fix for `as.mo()` * Small algorithm fix for `as.mo()`
* Removed viruses from data set `microorganisms.codes` and cleaned it up * Removed viruses from data set `microorganisms.codes` and cleaned it up
* Fix for `mo_shortname()` where species would not be determined correctly
#### Other #### Other
* Support for R 3.6.0 * Support for R 3.6.0

20
R/age.R
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@ -47,8 +47,8 @@ age <- function(x, reference = Sys.Date(), exact = FALSE) {
stop("`x` and `reference` must be of same length, or `reference` must be of length 1.") stop("`x` and `reference` must be of same length, or `reference` must be of length 1.")
} }
} }
x <- base::as.POSIXlt(x) x <- as.POSIXlt(x)
reference <- base::as.POSIXlt(reference) reference <- as.POSIXlt(reference)
# from https://stackoverflow.com/a/25450756/4575331 # from https://stackoverflow.com/a/25450756/4575331
years_gap <- reference$year - x$year years_gap <- reference$year - x$year
@ -59,13 +59,17 @@ age <- function(x, reference = Sys.Date(), exact = FALSE) {
# add decimals # add decimals
if (exact == TRUE) { if (exact == TRUE) {
# get dates of `x` when `x` would have the year of `reference` # get dates of `x` when `x` would have the year of `reference`
x_in_reference_year <- base::as.POSIXlt(paste0(format(reference, "%Y"), format(x, "-%m-%d"))) x_in_reference_year <- as.POSIXlt(paste0(format(reference, "%Y"), format(x, "-%m-%d")))
# get differences in days # get differences in days
n_days_x_rest <- base::as.double(base::difftime(reference, x_in_reference_year, units = "days")) n_days_x_rest <- as.double(difftime(reference, x_in_reference_year, units = "days"))
# get numbers of days the years of `reference` has for a reliable denominator # get numbers of days the years of `reference` has for a reliable denominator
n_days_reference_year <- base::as.POSIXlt(paste0(format(reference, "%Y"), "-12-31"))$yday + 1 n_days_reference_year <- as.POSIXlt(paste0(format(reference, "%Y"), "-12-31"))$yday + 1
# add decimal parts of year # add decimal parts of year
ages <- ages + (n_days_x_rest / n_days_reference_year) mod <- n_days_x_rest / n_days_reference_year
# negative mods are cases where `x_in_reference_year` > `reference` - so 'add' a year
mod[mod < 0] <- 1 + mod[mod < 0]
# and finally add to ages
ages <- ages + mod
} }
if (any(ages < 0, na.rm = TRUE)) { if (any(ages < 0, na.rm = TRUE)) {
@ -79,10 +83,6 @@ age <- function(x, reference = Sys.Date(), exact = FALSE) {
ages ages
} }
age_to_toDate <- function(age) {
}
#' Split ages into age groups #' Split ages into age groups
#' #'
#' Split ages into age groups defined by the \code{split} parameter. This allows for easier demographic (antimicrobial resistance) analysis. #' Split ages into age groups defined by the \code{split} parameter. This allows for easier demographic (antimicrobial resistance) analysis.

170
R/ggplot_rsi.R
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@ -21,7 +21,7 @@
#' AMR plots with \code{ggplot2} #' AMR plots with \code{ggplot2}
#' #'
#' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \code{\link[ggplot2]{ggplot}} functions. #' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \code{\link[ggplot2]{ggplot}2} functions.
#' @param data a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}}) #' @param data a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}})
#' @param position position adjustment of bars, either \code{"fill"} (default when \code{fun} is \code{\link{count_df}}), \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"} #' @param position position adjustment of bars, either \code{"fill"} (default when \code{fun} is \code{\link{count_df}}), \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"}
#' @param x variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable #' @param x variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable
@ -32,11 +32,17 @@
#' @param fun function to transform \code{data}, either \code{\link{count_df}} (default) or \code{\link{portion_df}} #' @param fun function to transform \code{data}, either \code{\link{count_df}} (default) or \code{\link{portion_df}}
#' @inheritParams portion #' @inheritParams portion
#' @param nrow (when using \code{facet}) number of rows #' @param nrow (when using \code{facet}) number of rows
#' @param datalabels show datalabels using \code{labels_rsi_count}, will at default only be shown when \code{fun = count_df} #' @param colours a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be \code{FALSE} to use default \code{ggplot2} colours.
#' @param datalabels show datalabels using \code{labels_rsi_count}, will only be shown when \code{fun = count_df}
#' @param datalabels.size size of the datalabels #' @param datalabels.size size of the datalabels
#' @param datalabels.colour colour of the datalabels #' @param datalabels.colour colour of the datalabels
#' @param title text to show as title of the plot
#' @param subtitle text to show as subtitle of the plot
#' @param caption text to show as caption of the plot
#' @param x.title text to show as x axis description
#' @param y.title text to show as y axis description
#' @param ... other parameters passed on to \code{geom_rsi} #' @param ... other parameters passed on to \code{geom_rsi}
#' @details At default, the names of antibiotics will be shown on the plots using \code{\link{ab_name}}. This can be set with the option \code{get_antibiotic_names} (a logical value), so change it e.g. to \code{FALSE} with \code{options(get_antibiotic_names = FALSE)}. #' @details At default, the names of antibiotics will be shown on the plots using \code{\link{ab_name}}. This can be set with the \code{translate_ab} parameter. See \code{\link{count_df}}.
#' #'
#' \strong{The functions}\cr #' \strong{The functions}\cr
#' \code{geom_rsi} will take any variable from the data that has an \code{rsi} class (created with \code{\link{as.rsi}}) using \code{fun} (\code{\link{count_df}} at default, can also be \code{\link{portion_df}}) and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis. #' \code{geom_rsi} will take any variable from the data that has an \code{rsi} class (created with \code{\link{as.rsi}}) using \code{fun} (\code{\link{count_df}} at default, can also be \code{\link{portion_df}}) and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.
@ -45,7 +51,7 @@
#' #'
#' \code{scale_y_percent} transforms the y axis to a 0 to 100\% range using \code{\link[ggplot2]{scale_continuous}}. #' \code{scale_y_percent} transforms the y axis to a 0 to 100\% range using \code{\link[ggplot2]{scale_continuous}}.
#' #'
#' \code{scale_rsi_colours} sets colours to the bars: green for S, yellow for I and red for R, using \code{\link[ggplot2]{scale_brewer}}. #' \code{scale_rsi_colours} sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using \code{\link[ggplot2]{scale_brewer}}.
#' #'
#' \code{theme_rsi} is a \code{ggplot \link[ggplot2]{theme}} with minimal distraction. #' \code{theme_rsi} is a \code{ggplot \link[ggplot2]{theme}} with minimal distraction.
#' #'
@ -65,7 +71,7 @@
#' geom_rsi() #' geom_rsi()
#' #'
#' # prettify the plot using some additional functions: #' # prettify the plot using some additional functions:
#' df <- septic_patients[, c("AMX", "NIT", "FOS", "TMP", "CIP")] #' df <- septic_patients %>% select(AMX, NIT, FOS, TMP, CIP)
#' ggplot(df) + #' ggplot(df) +
#' geom_rsi() + #' geom_rsi() +
#' scale_y_percent() + #' scale_y_percent() +
@ -92,6 +98,10 @@
#' linetype = 2, #' linetype = 2,
#' alpha = 0.25) #' alpha = 0.25)
#' #'
#' septic_patients %>%
#' select(AMX) %>%
#' ggplot_rsi(colours = c(SI = "yellow"))
#'
#' # resistance of ciprofloxacine per age group #' # resistance of ciprofloxacine per age group
#' septic_patients %>% #' septic_patients %>%
#' mutate(first_isolate = first_isolate(.)) %>% #' mutate(first_isolate = first_isolate(.)) %>%
@ -108,45 +118,45 @@
#' septic_patients %>% #' septic_patients %>%
#' select(AMX, NIT, FOS, TMP, CIP) %>% #' select(AMX, NIT, FOS, TMP, CIP) %>%
#' ggplot_rsi() + scale_fill_viridis_d() #' ggplot_rsi() + scale_fill_viridis_d()
#' # a shorter version which also adjusts data label colours:
#' septic_patients %>%
#' select(AMX, NIT, FOS, TMP, CIP) %>%
#' ggplot_rsi(colours = FALSE)
#' #'
#' #'
#' # it also supports groups (don't forget to use the group var on `x` or `facet`): #' # it also supports groups (don't forget to use the group var on `x` or `facet`):
#' septic_patients %>% #' septic_patients %>%
#' select(hospital_id, AMX, NIT, FOS, TMP, CIP) %>% #' select(hospital_id, AMX, NIT, FOS, TMP, CIP) %>%
#' group_by(hospital_id) %>% #' group_by(hospital_id) %>%
#' ggplot_rsi(x = hospital_id, #' ggplot_rsi(x = "hospital_id",
#' facet = Antibiotic, #' facet = "Antibiotic",
#' nrow = 1) + #' nrow = 1,
#' labs(title = "AMR of Anti-UTI Drugs Per Hospital", #' title = "AMR of Anti-UTI Drugs Per Hospital",
#' x = "Hospital") #' x.title = "Hospital",
#' datalabels = FALSE)
#' #'
#' # genuine analysis: check 2 most prevalent microorganisms #' # genuine analysis: check 3 most prevalent microorganisms
#' septic_patients %>% #' septic_patients %>%
#' # create new bacterial ID's, with all CoNS under the same group (Becker et al.) #' # create new bacterial ID's, with all CoNS under the same group (Becker et al.)
#' mutate(mo = as.mo(mo, Becker = TRUE)) %>% #' mutate(mo = as.mo(mo, Becker = TRUE)) %>%
#' # filter on top three bacterial ID's #' # filter on top three bacterial ID's
#' filter(mo %in% top_freq(freq(.$mo), 3)) %>% #' filter(mo %in% top_freq(freq(.$mo), 3)) %>%
#' # determine first isolates
#' mutate(first_isolate = first_isolate(.,
#' col_date = "date",
#' col_patient_id = "patient_id",
#' col_mo = "mo")) %>%
#' # filter on first isolates #' # filter on first isolates
#' filter(first_isolate == TRUE) %>% #' filter_first_isolate() %>%
#' # get short MO names (like "E. coli") #' # get short MO names (like "E. coli")
#' mutate(mo = mo_shortname(mo, Becker = TRUE)) %>% #' mutate(bug = mo_shortname(mo, Becker = TRUE)) %>%
#' # select this short name and some antiseptic drugs #' # select this short name and some antiseptic drugs
#' select(mo, CXM, GEN, CIP) %>% #' select(bug, CXM, GEN, CIP) %>%
#' # group by MO #' # group by MO
#' group_by(mo) %>% #' group_by(bug) %>%
#' # plot the thing, putting MOs on the facet #' # plot the thing, putting MOs on the facet
#' ggplot_rsi(x = Antibiotic, #' ggplot_rsi(x = "Antibiotic",
#' facet = mo, #' facet = "bug",
#' translate_ab = FALSE, #' translate_ab = FALSE,
#' nrow = 1) + #' nrow = 1,
#' labs(title = "AMR of Top Three Microorganisms In Blood Culture Isolates", #' title = "AMR of Top Three Microorganisms In Blood Culture Isolates",
#' subtitle = "Only First Isolates, CoNS grouped according to Becker et al. (2014)", #' subtitle = expression(paste("Only First Isolates, CoNS grouped according to Becker ", italic("et al."), " (2014)")),
#' x = "Microorganisms") #' x.title = "Antibiotic (EARS-Net code)")
#' } #' }
ggplot_rsi <- function(data, ggplot_rsi <- function(data,
position = NULL, position = NULL,
@ -162,9 +172,19 @@ ggplot_rsi <- function(data,
language = get_locale(), language = get_locale(),
fun = count_df, fun = count_df,
nrow = NULL, nrow = NULL,
datalabels = FALSE, colours = c(S = "#61a8ff",
datalabels.size = 3, SI = "#61a8ff",
datalabels.colour = "white", I = "#61f7ff",
IR = "#ff6961",
R = "#ff6961"),
datalabels = TRUE,
datalabels.size = 2.5,
datalabels.colour = "gray15",
title = NULL,
subtitle = NULL,
caption = NULL,
x.title = NULL,
y.title = NULL,
...) { ...) {
stopifnot_installed_package("ggplot2") stopifnot_installed_package("ggplot2")
@ -196,6 +216,10 @@ ggplot_rsi <- function(data,
facet <- NULL facet <- NULL
} }
if (is.null(position)) {
position <- "fill"
}
p <- ggplot2::ggplot(data = data) + p <- ggplot2::ggplot(data = data) +
geom_rsi(position = position, x = x, fill = fill, translate_ab = translate_ab, geom_rsi(position = position, x = x, fill = fill, translate_ab = translate_ab,
fun = fun, combine_SI = combine_SI, combine_IR = combine_IR, ...) + fun = fun, combine_SI = combine_SI, combine_IR = combine_IR, ...) +
@ -203,11 +227,13 @@ ggplot_rsi <- function(data,
if (fill == "Interpretation") { if (fill == "Interpretation") {
# set RSI colours # set RSI colours
p <- p + scale_rsi_colours() if (isFALSE(colours) & missing(datalabels.colour)) {
} # set datalabel colour to middle gray
if (is.null(position)) { datalabels.colour <- "gray50"
position <- "fill" }
p <- p + scale_rsi_colours(colours = colours)
} }
if (fun_name == "portion_df" if (fun_name == "portion_df"
| (fun_name == "count_df" & identical(position, "fill"))) { | (fun_name == "count_df" & identical(position, "fill"))) {
# portions, so use y scale with percentage # portions, so use y scale with percentage
@ -217,6 +243,9 @@ ggplot_rsi <- function(data,
if (fun_name == "count_df" & datalabels == TRUE) { if (fun_name == "count_df" & datalabels == TRUE) {
p <- p + labels_rsi_count(position = position, p <- p + labels_rsi_count(position = position,
x = x, x = x,
translate_ab = translate_ab,
combine_SI = combine_SI,
combine_IR = combine_IR,
datalabels.size = datalabels.size, datalabels.size = datalabels.size,
datalabels.colour = datalabels.colour) datalabels.colour = datalabels.colour)
} }
@ -225,6 +254,12 @@ ggplot_rsi <- function(data,
p <- p + facet_rsi(facet = facet, nrow = nrow) p <- p + facet_rsi(facet = facet, nrow = nrow)
} }
p <- p + ggplot2::labs(title = title,
subtitle = subtitle,
caption = caption,
x = x.title,
y = y.title)
p p
} }
@ -261,6 +296,10 @@ geom_rsi <- function(position = NULL,
} }
} }
if (identical(position, "fill")) {
position <- ggplot2::position_fill(vjust = 0.5, reverse = TRUE)
}
x <- x[1] x <- x[1]
# we work with aes_string later on # we work with aes_string later on
@ -296,7 +335,7 @@ facet_rsi <- function(facet = c("Interpretation", "Antibiotic"), nrow = NULL) {
stopifnot_installed_package("ggplot2") stopifnot_installed_package("ggplot2")
facet <- facet[1] facet <- facet[1]
# we work with aes_string later on # we work with aes_string later on
facet_deparse <- deparse(substitute(facet)) facet_deparse <- deparse(substitute(facet))
@ -331,37 +370,49 @@ scale_y_percent <- function(breaks = seq(0, 1, 0.1), limits = NULL) {
#' @rdname ggplot_rsi #' @rdname ggplot_rsi
#' @export #' @export
scale_rsi_colours <- function() { scale_rsi_colours <- function(colours = c(S = "#61a8ff",
SI = "#61a8ff",
I = "#61f7ff",
IR = "#ff6961",
R = "#ff6961")) {
stopifnot_installed_package("ggplot2") stopifnot_installed_package("ggplot2")
#ggplot2::scale_fill_brewer(palette = "RdYlGn") #ggplot2::scale_fill_brewer(palette = "RdYlGn")
#ggplot2::scale_fill_manual(values = c("#b22222", "#ae9c20", "#7cfc00")) #ggplot2::scale_fill_manual(values = c("#b22222", "#ae9c20", "#7cfc00"))
# mixed using https://www.colorhexa.com/b22222 if (!identical(colours, FALSE)) {
# and https://www.w3schools.com/colors/colors_mixer.asp original_cols <- c(S = "#61a8ff",
ggplot2::scale_fill_manual(values = c(S = "#22b222", SI = "#61a8ff",
SI = "#22b222", I = "#61f7ff",
I = "#548022", IR = "#ff6961",
IR = "#b22222", R = "#ff6961")
R = "#b22222")) colours <- replace(original_cols, names(colours), colours)
ggplot2::scale_fill_manual(values = colours)
}
} }
#' @rdname ggplot_rsi #' @rdname ggplot_rsi
#' @export #' @export
theme_rsi <- function() { theme_rsi <- function() {
stopifnot_installed_package("ggplot2") stopifnot_installed_package("ggplot2")
ggplot2::theme_minimal() + ggplot2::theme_minimal(base_size = 10) +
ggplot2::theme(panel.grid.major.x = ggplot2::element_blank(), ggplot2::theme(panel.grid.major.x = ggplot2::element_blank(),
panel.grid.minor = ggplot2::element_blank(), panel.grid.minor = ggplot2::element_blank(),
panel.grid.major.y = ggplot2::element_line(colour = "grey75")) panel.grid.major.y = ggplot2::element_line(colour = "grey75"),
# center title and subtitle
plot.title = ggplot2::element_text(hjust = 0.5),
plot.subtitle = ggplot2::element_text(hjust = 0.5))
} }
#' @rdname ggplot_rsi #' @rdname ggplot_rsi
#' @importFrom dplyr mutate %>% group_by_at
#' @export #' @export
labels_rsi_count <- function(position = NULL, labels_rsi_count <- function(position = NULL,
x = "Antibiotic", x = "Antibiotic",
translate_ab = "name",
combine_SI = TRUE,
combine_IR = FALSE,
datalabels.size = 3, datalabels.size = 3,
datalabels.colour = "white") { datalabels.colour = "gray15") {
stopifnot_installed_package("ggplot2") stopifnot_installed_package("ggplot2")
if (is.null(position)) { if (is.null(position)) {
position <- "fill" position <- "fill"
@ -369,23 +420,24 @@ labels_rsi_count <- function(position = NULL,
if (identical(position, "fill")) { if (identical(position, "fill")) {
position <- ggplot2::position_fill(vjust = 0.5, reverse = TRUE) position <- ggplot2::position_fill(vjust = 0.5, reverse = TRUE)
} }
x_name <- x
ggplot2::geom_text(mapping = ggplot2::aes_string(label = "lbl", ggplot2::geom_text(mapping = ggplot2::aes_string(label = "lbl",
x = x, x = x,
y = "Value"), y = "Value"),
position = position, position = position,
data = getlbls,
inherit.aes = FALSE, inherit.aes = FALSE,
size = datalabels.size, size = datalabels.size,
colour = datalabels.colour) colour = datalabels.colour,
lineheight = 0.75,
data = function(x) {
# labels are only shown when function is count_df,
# so no need parameterise it here
count_df(data = x,
translate_ab = translate_ab,
combine_SI = combine_SI,
combine_IR = combine_IR) %>%
group_by_at(x_name) %>%
mutate(lbl = paste0(percent(Value / sum(Value, na.rm = TRUE), force_zero = TRUE),
"\n(n=", Value, ")"))
})
} }
#' @importFrom dplyr %>% group_by mutate
getlbls <- function(data) {
data %>%
count_df() %>%
group_by(Antibiotic) %>%
mutate(lbl = paste0(percent(Value / sum(Value, na.rm = TRUE), force_zero = TRUE),
" (n=", Value, ")")) %>%
mutate(lbl = ifelse(lbl == "0.0% (n=0)", "", lbl))
}

73
R/mo_property.R
View File

@ -157,55 +157,32 @@ mo_shortname <- function(x, language = get_locale(), ...) {
Lancefield <- FALSE Lancefield <- FALSE
} }
shorten <- function(x) { # get result without transformations
# easiest: no transformations needed res1 <- AMR::as.mo(x, Becker = FALSE, Lancefield = FALSE, reference_df = dots$reference_df)
x <- mo_fullname(x, language = "en") # and result with transformations
# shorten for the ones that have a space: shorten first word and write out second word res2 <- suppressWarnings(AMR::as.mo(res1, ...))
shorten_these <- x %like% " " & !x %like% "Streptococcus group " res2_fullname <- mo_fullname(res2, language = language)
x[shorten_these] <- paste0(substr(x[shorten_these], 1, 1), res2_fullname[res2_fullname %like% " \\(CoNS\\)"] <- "CoNS"
". ", res2_fullname[res2_fullname %like% " \\(CoPS\\)"] <- "CoPS"
x[shorten_these] %>% res2_fullname[res2_fullname %like% " \\(KNS\\)"] <- "KNS"
strsplit(" ", fixed = TRUE) %>% res2_fullname[res2_fullname %like% " \\(KPS\\)"] <- "KPS"
unlist() %>% res2_fullname[res2_fullname %like% " \\(CNS\\)"] <- "CNS"
.[2]) res2_fullname[res2_fullname %like% " \\(CPS\\)"] <- "CPS"
x res2_fullname[res2_fullname %like% " \\(SCN\\)"] <- "SCN"
} res2_fullname <- gsub("Streptococcus (group|Gruppe|gruppe|groep|grupo|gruppo|groupe) (.)",
"G\\2S",
if (isFALSE(Becker) & isFALSE(Lancefield)) { res2_fullname) # turn "Streptococcus group A" and "Streptococcus grupo A" to "GAS"
result <- shorten(x) res2_fullname_vector <- res2_fullname[res2_fullname == mo_fullname(res1)]
res2_fullname[res2_fullname == mo_fullname(res1)] <- paste0(substr(mo_genus(res2_fullname_vector), 1, 1),
} else { ". ",
# get result without transformations suppressWarnings(mo_species(res2_fullname_vector)))
res1 <- AMR::as.mo(x, Becker = FALSE, Lancefield = FALSE, reference_df = dots$reference_df) if (sum(res1 == res2, na.rm = TRUE) > 0) {
# and result with transformations res1[res1 == res2] <- paste0(substr(mo_genus(res1[res1 == res2]), 1, 1),
res2 <- suppressWarnings(AMR::as.mo(res1, ...)) ". ",
if (res1 == res2 suppressWarnings(mo_species(res1[res1 == res2])))
& !res1 %like% "^B_STRPT_GR") {
result <- shorten(x)
} else {
res2_fullname <- mo_fullname(res2, language = language)
res2_fullname[res2_fullname %like% " \\(CoNS\\)"] <- "CoNS"
res2_fullname[res2_fullname %like% " \\(CoPS\\)"] <- "CoPS"
res2_fullname[res2_fullname %like% " \\(KNS\\)"] <- "KNS"
res2_fullname[res2_fullname %like% " \\(KPS\\)"] <- "KPS"
res2_fullname[res2_fullname %like% " \\(CNS\\)"] <- "CNS"
res2_fullname[res2_fullname %like% " \\(CPS\\)"] <- "CPS"
res2_fullname <- gsub("Streptococcus (group|Gruppe|gruppe|groep|grupo|gruppo|groupe) (.)",
"G\\2S",
res2_fullname) # turn "Streptococcus group A" and "Streptococcus grupo A" to "GAS"
res2_fullname_vector <- res2_fullname[res2_fullname == mo_fullname(res1)]
res2_fullname[res2_fullname == mo_fullname(res1)] <- paste0(substr(mo_genus(res2_fullname_vector), 1, 1),
". ",
suppressWarnings(mo_species(res2_fullname_vector)))
if (sum(res1 == res2, na.rm = TRUE) > 0) {
res1[res1 == res2] <- paste0(substr(mo_genus(res1[res1 == res2]), 1, 1),
". ",
suppressWarnings(mo_species(res1[res1 == res2])))
}
res1[res1 != res2] <- res2_fullname
result <- as.character(res1)
}
} }
res1[res1 != res2] <- res2_fullname
result <- as.character(res1)
t(result, language = language) t(result, language = language)
} }

10
_pkgdown.yml
View File

@ -19,9 +19,12 @@
# Visit our website for more info: https://msberends.gitlab.io/AMR. # # Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== # # ==================================================================== #
url: 'https://msberends.gitlab.io/AMR'
title: 'AMR (for R)' title: 'AMR (for R)'
url: 'https://msberends.gitlab.io/AMR'
development:
mode: release # improves indexing by search engines
news:
one_page: true
navbar: navbar:
title: 'AMR (for R)' title: 'AMR (for R)'
@ -177,9 +180,6 @@ authors:
Bhanu N. M. Sinha: Bhanu N. M. Sinha:
href: https://www.rug.nl/staff/b.sinha/ href: https://www.rug.nl/staff/b.sinha/
development:
mode: release # improves indexing by search engines
template: template:
assets: pkgdown/logos # use logos in this folder assets: pkgdown/logos # use logos in this folder
params: params:

2
docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9045</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9045</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9045</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
</span> </span>
</div> </div>

2
docs/index.html
View File

@ -42,7 +42,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9045</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
</span> </span>
</div> </div>

9
docs/news/index.html
View File

@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9045</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
</span> </span>
</div> </div>
@ -278,6 +278,12 @@
Please create an issue in one of our repositories if you want additions in this file.</li> Please create an issue in one of our repositories if you want additions in this file.</li>
</ul> </ul>
</li> </li>
<li>Improvements to plotting AMR results with <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code>:
<ul>
<li>New parameter <code>colours</code> to set the bar colours</li>
<li>New parameters <code>title</code>, <code>subtitle</code>, <code>caption</code>, <code>x.title</code> and <code>y.title</code> to set titles and axis descriptions</li>
</ul>
</li>
<li>Improved intelligence of looking up antibiotic tables in data set using <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code> <li>Improved intelligence of looking up antibiotic tables in data set using <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
</li> </li>
<li>Added ~5,000 more old taxonomic names to the <code>microorganisms.old</code> data set, which leads to better results finding when using the <code><a href="../reference/as.mo.html">as.mo()</a></code> function</li> <li>Added ~5,000 more old taxonomic names to the <code>microorganisms.old</code> data set, which leads to better results finding when using the <code><a href="../reference/as.mo.html">as.mo()</a></code> function</li>
@ -316,6 +322,7 @@ Please create an issue in one of our repositories if you want additions in this
<li>Small algorithm fix for <code><a href="../reference/as.mo.html">as.mo()</a></code> <li>Small algorithm fix for <code><a href="../reference/as.mo.html">as.mo()</a></code>
</li> </li>
<li>Removed viruses from data set <code>microorganisms.codes</code> and cleaned it up</li> <li>Removed viruses from data set <code>microorganisms.codes</code> and cleaned it up</li>
<li>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> where species would not be determined correctly</li>
</ul> </ul>
</div> </div>
<div id="other" class="section level4"> <div id="other" class="section level4">

97
docs/reference/ggplot_rsi.html
View File

@ -47,7 +47,7 @@
<script src="../extra.js"></script> <script src="../extra.js"></script>
<meta property="og:title" content="AMR plots with <code>ggplot2</code> — ggplot_rsi" /> <meta property="og:title" content="AMR plots with <code>ggplot2</code> — ggplot_rsi" />
<meta property="og:description" content="Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal ggplot functions." /> <meta property="og:description" content="Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal ggplot2 functions." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" /> <meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" /> <meta name="twitter:card" content="summary" />
@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
</span> </span>
</div> </div>
@ -244,7 +244,7 @@
<div class="ref-description"> <div class="ref-description">
<p>Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal <code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code> functions.</p> <p>Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal <code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a>2</code> functions.</p>
</div> </div>
@ -252,8 +252,11 @@
<span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"Interpretation"</span>, <span class='kw'>facet</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>), <span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"Interpretation"</span>, <span class='kw'>facet</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>),
<span class='kw'>limits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>limits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>count_df</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>count_df</span>,
<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>datalabels</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>datalabels.size</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>colours</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>S</span> <span class='kw'>=</span> <span class='st'>"#61a8ff"</span>, <span class='kw'>SI</span> <span class='kw'>=</span> <span class='st'>"#61a8ff"</span>, <span class='kw'>I</span> <span class='kw'>=</span>
<span class='kw'>datalabels.colour</span> <span class='kw'>=</span> <span class='st'>"white"</span>, <span class='no'>...</span>) <span class='st'>"#61f7ff"</span>, <span class='kw'>IR</span> <span class='kw'>=</span> <span class='st'>"#ff6961"</span>, <span class='kw'>R</span> <span class='kw'>=</span> <span class='st'>"#ff6961"</span>), <span class='kw'>datalabels</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>datalabels.size</span> <span class='kw'>=</span> <span class='fl'>2.5</span>, <span class='kw'>datalabels.colour</span> <span class='kw'>=</span> <span class='st'>"gray15"</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>subtitle</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>caption</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x.title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>y.title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='no'>...</span>)
<span class='fu'>geom_rsi</span>(<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Antibiotic"</span>, <span class='st'>"Interpretation"</span>), <span class='fu'>geom_rsi</span>(<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Antibiotic"</span>, <span class='st'>"Interpretation"</span>),
<span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"Interpretation"</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"Interpretation"</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>,
@ -264,12 +267,14 @@
<span class='fu'>scale_y_percent</span>(<span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>), <span class='kw'>limits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>) <span class='fu'>scale_y_percent</span>(<span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>), <span class='kw'>limits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
<span class='fu'>scale_rsi_colours</span>() <span class='fu'>scale_rsi_colours</span>(<span class='kw'>colours</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>S</span> <span class='kw'>=</span> <span class='st'>"#61a8ff"</span>, <span class='kw'>SI</span> <span class='kw'>=</span> <span class='st'>"#61a8ff"</span>, <span class='kw'>I</span> <span class='kw'>=</span>
<span class='st'>"#61f7ff"</span>, <span class='kw'>IR</span> <span class='kw'>=</span> <span class='st'>"#ff6961"</span>, <span class='kw'>R</span> <span class='kw'>=</span> <span class='st'>"#ff6961"</span>))
<span class='fu'>theme_rsi</span>() <span class='fu'>theme_rsi</span>()
<span class='fu'>labels_rsi_count</span>(<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Antibiotic"</span>, <span class='fu'>labels_rsi_count</span>(<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Antibiotic"</span>,
<span class='kw'>datalabels.size</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>datalabels.colour</span> <span class='kw'>=</span> <span class='st'>"white"</span>)</pre> <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>datalabels.size</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>datalabels.colour</span> <span class='kw'>=</span> <span class='st'>"gray15"</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments"> <table class="ref-arguments">
@ -326,9 +331,13 @@
<th>nrow</th> <th>nrow</th>
<td><p>(when using <code>facet</code>) number of rows</p></td> <td><p>(when using <code>facet</code>) number of rows</p></td>
</tr> </tr>
<tr>
<th>colours</th>
<td><p>a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be <code>FALSE</code> to use default <code>ggplot2</code> colours.</p></td>
</tr>
<tr> <tr>
<th>datalabels</th> <th>datalabels</th>
<td><p>show datalabels using <code>labels_rsi_count</code>, will at default only be shown when <code>fun = count_df</code></p></td> <td><p>show datalabels using <code>labels_rsi_count</code>, will only be shown when <code>fun = count_df</code></p></td>
</tr> </tr>
<tr> <tr>
<th>datalabels.size</th> <th>datalabels.size</th>
@ -338,6 +347,26 @@
<th>datalabels.colour</th> <th>datalabels.colour</th>
<td><p>colour of the datalabels</p></td> <td><p>colour of the datalabels</p></td>
</tr> </tr>
<tr>
<th>title</th>
<td><p>text to show as title of the plot</p></td>
</tr>
<tr>
<th>subtitle</th>
<td><p>text to show as subtitle of the plot</p></td>
</tr>
<tr>
<th>caption</th>
<td><p>text to show as caption of the plot</p></td>
</tr>
<tr>
<th>x.title</th>
<td><p>text to show as x axis description</p></td>
</tr>
<tr>
<th>y.title</th>
<td><p>text to show as y axis description</p></td>
</tr>
<tr> <tr>
<th>...</th> <th>...</th>
<td><p>other parameters passed on to <code>geom_rsi</code></p></td> <td><p>other parameters passed on to <code>geom_rsi</code></p></td>
@ -346,12 +375,12 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>At default, the names of antibiotics will be shown on the plots using <code><a href='ab_property.html'>ab_name</a></code>. This can be set with the option <code>get_antibiotic_names</code> (a logical value), so change it e.g. to <code>FALSE</code> with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>options(get_antibiotic_names = FALSE)</a></code>.</p> <p>At default, the names of antibiotics will be shown on the plots using <code><a href='ab_property.html'>ab_name</a></code>. This can be set with the <code>translate_ab</code> parameter. See <code><a href='count.html'>count_df</a></code>.</p>
<p><strong>The functions</strong><br /> <p><strong>The functions</strong><br />
<code>geom_rsi</code> will take any variable from the data that has an <code>rsi</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) using <code>fun</code> (<code><a href='count.html'>count_df</a></code> at default, can also be <code><a href='portion.html'>portion_df</a></code>) and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p> <code>geom_rsi</code> will take any variable from the data that has an <code>rsi</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) using <code>fun</code> (<code><a href='count.html'>count_df</a></code> at default, can also be <code><a href='portion.html'>portion_df</a></code>) and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p>
<p><code>facet_rsi</code> creates 2d plots (at default based on S/I/R) using <code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/facet_wrap'>facet_wrap</a></code>.</p> <p><code>facet_rsi</code> creates 2d plots (at default based on S/I/R) using <code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/facet_wrap'>facet_wrap</a></code>.</p>
<p><code>scale_y_percent</code> transforms the y axis to a 0 to 100% range using <code>scale_continuous</code>.</p> <p><code>scale_y_percent</code> transforms the y axis to a 0 to 100% range using <code>scale_continuous</code>.</p>
<p><code>scale_rsi_colours</code> sets colours to the bars: green for S, yellow for I and red for R, using <code>scale_brewer</code>.</p> <p><code>scale_rsi_colours</code> sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using <code>scale_brewer</code>.</p>
<p><code>theme_rsi</code> is a <code>ggplot <a href='https://www.rdocumentation.org/packages/ggplot2/topics/theme'>theme</a></code> with minimal distraction.</p> <p><code>theme_rsi</code> is a <code>ggplot <a href='https://www.rdocumentation.org/packages/ggplot2/topics/theme'>theme</a></code> with minimal distraction.</p>
<p><code>labels_rsi_count</code> print datalabels on the bars with percentage and amount of isolates using <code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/geom_text'>geom_text</a></code></p> <p><code>labels_rsi_count</code> print datalabels on the bars with percentage and amount of isolates using <code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/geom_text'>geom_text</a></code></p>
<p><code>ggplot_rsi</code> is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (<code>%&gt;%</code>). See Examples.</p> <p><code>ggplot_rsi</code> is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (<code>%&gt;%</code>). See Examples.</p>
@ -372,7 +401,7 @@
<span class='fu'>geom_rsi</span>() <span class='fu'>geom_rsi</span>()
<span class='co'># prettify the plot using some additional functions:</span> <span class='co'># prettify the plot using some additional functions:</span>
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span>[, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"AMX"</span>, <span class='st'>"NIT"</span>, <span class='st'>"FOS"</span>, <span class='st'>"TMP"</span>, <span class='st'>"CIP"</span>)] <span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></span>(<span class='no'>df</span>) + <span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></span>(<span class='no'>df</span>) +
<span class='fu'>geom_rsi</span>() + <span class='fu'>geom_rsi</span>() +
<span class='fu'>scale_y_percent</span>() + <span class='fu'>scale_y_percent</span>() +
@ -399,6 +428,10 @@
<span class='kw'>linetype</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>linetype</span> <span class='kw'>=</span> <span class='fl'>2</span>,
<span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.25</span>) <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.25</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>colours</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>SI</span> <span class='kw'>=</span> <span class='st'>"yellow"</span>))
<span class='co'># resistance of ciprofloxacine per age group</span> <span class='co'># resistance of ciprofloxacine per age group</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
@ -414,45 +447,45 @@
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>() + <span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/scale_viridis'>scale_fill_viridis_d</a></span>() <span class='fu'>ggplot_rsi</span>() + <span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/scale_viridis'>scale_fill_viridis_d</a></span>()
<span class='co'># a shorter version which also adjusts data label colours:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>colours</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># it also supports groups (don't forget to use the group var on `x` or `facet`):</span> <span class='co'># it also supports groups (don't forget to use the group var on `x` or `facet`):</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>hospital_id</span>, <span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"hospital_id"</span>,
<span class='kw'>facet</span> <span class='kw'>=</span> <span class='no'>Antibiotic</span>, <span class='kw'>facet</span> <span class='kw'>=</span> <span class='st'>"Antibiotic"</span>,
<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>) + <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>,
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/labs'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>,
<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Hospital"</span>) <span class='kw'>x.title</span> <span class='kw'>=</span> <span class='st'>"Hospital"</span>,
<span class='kw'>datalabels</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># genuine analysis: check 2 most prevalent microorganisms</span> <span class='co'># genuine analysis: check 3 most prevalent microorganisms</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='co'># create new bacterial ID's, with all CoNS under the same group (Becker et al.)</span> <span class='co'># create new bacterial ID's, with all CoNS under the same group (Becker et al.)</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># filter on top three bacterial ID's</span> <span class='co'># filter on top three bacterial ID's</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>%in%</span> <span class='fu'><a href='freq.html'>top_freq</a></span>(<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>.</span>$<span class='no'>mo</span>), <span class='fl'>3</span>)) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>%in%</span> <span class='fu'><a href='freq.html'>top_freq</a></span>(<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>.</span>$<span class='no'>mo</span>), <span class='fl'>3</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># determine first isolates</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>,
<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
<span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='st'>"patient_id"</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='st'>"mo"</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># filter on first isolates</span> <span class='co'># filter on first isolates</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='kw'>%&gt;%</span>
<span class='co'># get short MO names (like "E. coli")</span> <span class='co'># get short MO names (like "E. coli")</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>bug</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># select this short name and some antiseptic drugs</span> <span class='co'># select this short name and some antiseptic drugs</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>, <span class='no'>CXM</span>, <span class='no'>GEN</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>bug</span>, <span class='no'>CXM</span>, <span class='no'>GEN</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='co'># group by MO</span> <span class='co'># group by MO</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>bug</span>) <span class='kw'>%&gt;%</span>
<span class='co'># plot the thing, putting MOs on the facet</span> <span class='co'># plot the thing, putting MOs on the facet</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>Antibiotic</span>, <span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Antibiotic"</span>,
<span class='kw'>facet</span> <span class='kw'>=</span> <span class='no'>mo</span>, <span class='kw'>facet</span> <span class='kw'>=</span> <span class='st'>"bug"</span>,
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>) + <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>,
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/labs'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Top Three Microorganisms In Blood Culture Isolates"</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Top Three Microorganisms In Blood Culture Isolates"</span>,
<span class='kw'>subtitle</span> <span class='kw'>=</span> <span class='st'>"Only First Isolates, CoNS grouped according to Becker et al. (2014)"</span>, <span class='kw'>subtitle</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/expression'>expression</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"Only First Isolates, CoNS grouped according to Becker "</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/grDevices/topics/plotmath'>italic</a></span>(<span class='st'>"et al."</span>), <span class='st'>" (2014)"</span>)),
<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Microorganisms"</span>) <span class='kw'>x.title</span> <span class='kw'>=</span> <span class='st'>"Antibiotic (Ears-Net code)"</span>)
<span class='co'># }</span></pre> <span class='co'># }</span></pre>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

2
docs/reference/index.html
View File

@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9045</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9046</span>
</span> </span>
</div> </div>

81
man/ggplot_rsi.Rd
View File

@ -14,8 +14,11 @@ ggplot_rsi(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,
combine_IR = FALSE, language = get_locale(), fun = count_df, combine_IR = FALSE, language = get_locale(), fun = count_df,
nrow = NULL, datalabels = FALSE, datalabels.size = 3, nrow = NULL, colours = c(S = "#61a8ff", SI = "#61a8ff", I =
datalabels.colour = "white", ...) "#61f7ff", IR = "#ff6961", R = "#ff6961"), datalabels = TRUE,
datalabels.size = 2.5, datalabels.colour = "gray15", title = NULL,
subtitle = NULL, caption = NULL, x.title = NULL, y.title = NULL,
...)
geom_rsi(position = NULL, x = c("Antibiotic", "Interpretation"), geom_rsi(position = NULL, x = c("Antibiotic", "Interpretation"),
fill = "Interpretation", translate_ab = "name", fill = "Interpretation", translate_ab = "name",
@ -26,12 +29,14 @@ facet_rsi(facet = c("Interpretation", "Antibiotic"), nrow = NULL)
scale_y_percent(breaks = seq(0, 1, 0.1), limits = NULL) scale_y_percent(breaks = seq(0, 1, 0.1), limits = NULL)
scale_rsi_colours() scale_rsi_colours(colours = c(S = "#61a8ff", SI = "#61a8ff", I =
"#61f7ff", IR = "#ff6961", R = "#ff6961"))
theme_rsi() theme_rsi()
labels_rsi_count(position = NULL, x = "Antibiotic", labels_rsi_count(position = NULL, x = "Antibiotic",
datalabels.size = 3, datalabels.colour = "white") translate_ab = "name", combine_SI = TRUE, combine_IR = FALSE,
datalabels.size = 3, datalabels.colour = "gray15")
} }
\arguments{ \arguments{
\item{data}{a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}})} \item{data}{a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}})}
@ -60,19 +65,31 @@ labels_rsi_count(position = NULL, x = "Antibiotic",
\item{nrow}{(when using \code{facet}) number of rows} \item{nrow}{(when using \code{facet}) number of rows}
\item{datalabels}{show datalabels using \code{labels_rsi_count}, will at default only be shown when \code{fun = count_df}} \item{colours}{a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be \code{FALSE} to use default \code{ggplot2} colours.}
\item{datalabels}{show datalabels using \code{labels_rsi_count}, will only be shown when \code{fun = count_df}}
\item{datalabels.size}{size of the datalabels} \item{datalabels.size}{size of the datalabels}
\item{datalabels.colour}{colour of the datalabels} \item{datalabels.colour}{colour of the datalabels}
\item{title}{text to show as title of the plot}
\item{subtitle}{text to show as subtitle of the plot}
\item{caption}{text to show as caption of the plot}
\item{x.title}{text to show as x axis description}
\item{y.title}{text to show as y axis description}
\item{...}{other parameters passed on to \code{geom_rsi}} \item{...}{other parameters passed on to \code{geom_rsi}}
} }
\description{ \description{
Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \code{\link[ggplot2]{ggplot}} functions. Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \code{\link[ggplot2]{ggplot}2} functions.
} }
\details{ \details{
At default, the names of antibiotics will be shown on the plots using \code{\link{ab_name}}. This can be set with the option \code{get_antibiotic_names} (a logical value), so change it e.g. to \code{FALSE} with \code{options(get_antibiotic_names = FALSE)}. At default, the names of antibiotics will be shown on the plots using \code{\link{ab_name}}. This can be set with the \code{translate_ab} parameter. See \code{\link{count_df}}.
\strong{The functions}\cr \strong{The functions}\cr
\code{geom_rsi} will take any variable from the data that has an \code{rsi} class (created with \code{\link{as.rsi}}) using \code{fun} (\code{\link{count_df}} at default, can also be \code{\link{portion_df}}) and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis. \code{geom_rsi} will take any variable from the data that has an \code{rsi} class (created with \code{\link{as.rsi}}) using \code{fun} (\code{\link{count_df}} at default, can also be \code{\link{portion_df}}) and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.
@ -81,7 +98,7 @@ At default, the names of antibiotics will be shown on the plots using \code{\lin
\code{scale_y_percent} transforms the y axis to a 0 to 100\% range using \code{\link[ggplot2]{scale_continuous}}. \code{scale_y_percent} transforms the y axis to a 0 to 100\% range using \code{\link[ggplot2]{scale_continuous}}.
\code{scale_rsi_colours} sets colours to the bars: green for S, yellow for I and red for R, using \code{\link[ggplot2]{scale_brewer}}. \code{scale_rsi_colours} sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using \code{\link[ggplot2]{scale_brewer}}.
\code{theme_rsi} is a \code{ggplot \link[ggplot2]{theme}} with minimal distraction. \code{theme_rsi} is a \code{ggplot \link[ggplot2]{theme}} with minimal distraction.
@ -103,7 +120,7 @@ ggplot(septic_patients \%>\% select(AMX, NIT, FOS, TMP, CIP)) +
geom_rsi() geom_rsi()
# prettify the plot using some additional functions: # prettify the plot using some additional functions:
df <- septic_patients[, c("AMX", "NIT", "FOS", "TMP", "CIP")] df <- septic_patients \%>\% select(AMX, NIT, FOS, TMP, CIP)
ggplot(df) + ggplot(df) +
geom_rsi() + geom_rsi() +
scale_y_percent() + scale_y_percent() +
@ -130,6 +147,10 @@ septic_patients \%>\%
linetype = 2, linetype = 2,
alpha = 0.25) alpha = 0.25)
septic_patients \%>\%
select(AMX) \%>\%
ggplot_rsi(colours = c(SI = "yellow"))
# resistance of ciprofloxacine per age group # resistance of ciprofloxacine per age group
septic_patients \%>\% septic_patients \%>\%
mutate(first_isolate = first_isolate(.)) \%>\% mutate(first_isolate = first_isolate(.)) \%>\%
@ -146,44 +167,44 @@ septic_patients \%>\%
septic_patients \%>\% septic_patients \%>\%
select(AMX, NIT, FOS, TMP, CIP) \%>\% select(AMX, NIT, FOS, TMP, CIP) \%>\%
ggplot_rsi() + scale_fill_viridis_d() ggplot_rsi() + scale_fill_viridis_d()
# a shorter version which also adjusts data label colours:
septic_patients \%>\%
select(AMX, NIT, FOS, TMP, CIP) \%>\%
ggplot_rsi(colours = FALSE)
# it also supports groups (don't forget to use the group var on `x` or `facet`): # it also supports groups (don't forget to use the group var on `x` or `facet`):
septic_patients \%>\% septic_patients \%>\%
select(hospital_id, AMX, NIT, FOS, TMP, CIP) \%>\% select(hospital_id, AMX, NIT, FOS, TMP, CIP) \%>\%
group_by(hospital_id) \%>\% group_by(hospital_id) \%>\%
ggplot_rsi(x = hospital_id, ggplot_rsi(x = "hospital_id",
facet = Antibiotic, facet = "Antibiotic",
nrow = 1) + nrow = 1,
labs(title = "AMR of Anti-UTI Drugs Per Hospital", title = "AMR of Anti-UTI Drugs Per Hospital",
x = "Hospital") x.title = "Hospital",
datalabels = FALSE)
# genuine analysis: check 2 most prevalent microorganisms # genuine analysis: check 3 most prevalent microorganisms
septic_patients \%>\% septic_patients \%>\%
# create new bacterial ID's, with all CoNS under the same group (Becker et al.) # create new bacterial ID's, with all CoNS under the same group (Becker et al.)
mutate(mo = as.mo(mo, Becker = TRUE)) \%>\% mutate(mo = as.mo(mo, Becker = TRUE)) \%>\%
# filter on top three bacterial ID's # filter on top three bacterial ID's
filter(mo \%in\% top_freq(freq(.$mo), 3)) \%>\% filter(mo \%in\% top_freq(freq(.$mo), 3)) \%>\%
# determine first isolates
mutate(first_isolate = first_isolate(.,
col_date = "date",
col_patient_id = "patient_id",
col_mo = "mo")) \%>\%
# filter on first isolates # filter on first isolates
filter(first_isolate == TRUE) \%>\% filter_first_isolate() \%>\%
# get short MO names (like "E. coli") # get short MO names (like "E. coli")
mutate(mo = mo_shortname(mo, Becker = TRUE)) \%>\% mutate(bug = mo_shortname(mo, Becker = TRUE)) \%>\%
# select this short name and some antiseptic drugs # select this short name and some antiseptic drugs
select(mo, CXM, GEN, CIP) \%>\% select(bug, CXM, GEN, CIP) \%>\%
# group by MO # group by MO
group_by(mo) \%>\% group_by(bug) \%>\%
# plot the thing, putting MOs on the facet # plot the thing, putting MOs on the facet
ggplot_rsi(x = Antibiotic, ggplot_rsi(x = "Antibiotic",
facet = mo, facet = "bug",
translate_ab = FALSE, translate_ab = FALSE,
nrow = 1) + nrow = 1,
labs(title = "AMR of Top Three Microorganisms In Blood Culture Isolates", title = "AMR of Top Three Microorganisms In Blood Culture Isolates",
subtitle = "Only First Isolates, CoNS grouped according to Becker et al. (2014)", subtitle = expression(paste("Only First Isolates, CoNS grouped according to Becker ", italic("et al."), " (2014)")),
x = "Microorganisms") x.title = "Antibiotic (EARS-Net code)")
} }
} }

2
tests/testthat/test-freq.R
View File

@ -79,6 +79,8 @@ test_that("frequency table works", {
Sys.time() - runif(5, min = 0, max = 60 * 60 * 24), Sys.time() - runif(5, min = 0, max = 60 * 60 * 24),
units = "hours"))))) units = "hours")))))
expect_output(print(freq(septic_patients$age)[,1:3]))
library(dplyr) library(dplyr)
expect_output(septic_patients %>% select(1:2) %>% freq() %>% print()) expect_output(septic_patients %>% select(1:2) %>% freq() %>% print())
expect_output(septic_patients %>% select(1:3) %>% freq() %>% print()) expect_output(septic_patients %>% select(1:3) %>% freq() %>% print())