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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
Version: 0.6.1.9045
Version: 0.6.1.9046
Date: 2019-05-31
Title: Antimicrobial Resistance Analysis
Authors@R: c(

4
NEWS.md
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@ -22,6 +22,9 @@
system.file("translations.tsv", package = "AMR")
```
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()`
* 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.
@ -50,6 +53,7 @@
* Function `as.mo()` now gently interprets any number of whitespace characters (like tabs) as one space
* Small algorithm fix for `as.mo()`
* Removed viruses from data set `microorganisms.codes` and cleaned it up
* Fix for `mo_shortname()` where species would not be determined correctly
#### Other
* 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.")
}
}
x <- base::as.POSIXlt(x)
reference <- base::as.POSIXlt(reference)
x <- as.POSIXlt(x)
reference <- as.POSIXlt(reference)
# from https://stackoverflow.com/a/25450756/4575331
years_gap <- reference$year - x$year
@ -59,13 +59,17 @@ age <- function(x, reference = Sys.Date(), exact = FALSE) {
# add decimals
if (exact == TRUE) {
# 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
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
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
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)) {
@ -79,10 +83,6 @@ age <- function(x, reference = Sys.Date(), exact = FALSE) {
ages
}
age_to_toDate <- function(age) {
}
#' Split ages into age groups
#'
#' 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}
#'
#' 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 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
@ -32,11 +32,17 @@
#' @param fun function to transform \code{data}, either \code{\link{count_df}} (default) or \code{\link{portion_df}}
#' @inheritParams portion
#' @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.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}
#' @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
#' \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_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.
#'
@ -65,7 +71,7 @@
#' geom_rsi()
#'
#' # 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) +
#' geom_rsi() +
#' scale_y_percent() +
@ -92,6 +98,10 @@
#' linetype = 2,
#' alpha = 0.25)
#'
#' septic_patients %>%
#' select(AMX) %>%
#' ggplot_rsi(colours = c(SI = "yellow"))
#'
#' # resistance of ciprofloxacine per age group
#' septic_patients %>%
#' mutate(first_isolate = first_isolate(.)) %>%
@ -108,45 +118,45 @@
#' septic_patients %>%
#' select(AMX, NIT, FOS, TMP, CIP) %>%
#' 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`):
#' septic_patients %>%
#' select(hospital_id, AMX, NIT, FOS, TMP, CIP) %>%
#' group_by(hospital_id) %>%
#' ggplot_rsi(x = hospital_id,
#' facet = Antibiotic,
#' nrow = 1) +
#' labs(title = "AMR of Anti-UTI Drugs Per Hospital",
#' x = "Hospital")
#' ggplot_rsi(x = "hospital_id",
#' facet = "Antibiotic",
#' nrow = 1,
#' title = "AMR of Anti-UTI Drugs Per Hospital",
#' x.title = "Hospital",
#' datalabels = FALSE)
#'
#' # genuine analysis: check 2 most prevalent microorganisms
#' # genuine analysis: check 3 most prevalent microorganisms
#' septic_patients %>%
#' # create new bacterial ID's, with all CoNS under the same group (Becker et al.)
#' mutate(mo = as.mo(mo, Becker = TRUE)) %>%
#' # filter on top three bacterial ID's
#' 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(first_isolate == TRUE) %>%
#' filter_first_isolate() %>%
#' # 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(mo, CXM, GEN, CIP) %>%
#' select(bug, CXM, GEN, CIP) %>%
#' # group by MO
#' group_by(mo) %>%
#' group_by(bug) %>%
#' # plot the thing, putting MOs on the facet
#' ggplot_rsi(x = Antibiotic,
#' facet = mo,
#' ggplot_rsi(x = "Antibiotic",
#' facet = "bug",
#' translate_ab = FALSE,
#' nrow = 1) +
#' labs(title = "AMR of Top Three Microorganisms In Blood Culture Isolates",
#' subtitle = "Only First Isolates, CoNS grouped according to Becker et al. (2014)",
#' x = "Microorganisms")
#' nrow = 1,
#' title = "AMR of Top Three Microorganisms In Blood Culture Isolates",
#' subtitle = expression(paste("Only First Isolates, CoNS grouped according to Becker ", italic("et al."), " (2014)")),
#' x.title = "Antibiotic (EARS-Net code)")
#' }
ggplot_rsi <- function(data,
position = NULL,
@ -162,9 +172,19 @@ ggplot_rsi <- function(data,
language = get_locale(),
fun = count_df,
nrow = NULL,
datalabels = FALSE,
datalabels.size = 3,
datalabels.colour = "white",
colours = c(S = "#61a8ff",
SI = "#61a8ff",
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")
@ -196,6 +216,10 @@ ggplot_rsi <- function(data,
facet <- NULL
}
if (is.null(position)) {
position <- "fill"
}
p <- ggplot2::ggplot(data = data) +
geom_rsi(position = position, x = x, fill = fill, translate_ab = translate_ab,
fun = fun, combine_SI = combine_SI, combine_IR = combine_IR, ...) +
@ -203,11 +227,13 @@ ggplot_rsi <- function(data,
if (fill == "Interpretation") {
# set RSI colours
p <- p + scale_rsi_colours()
}
if (is.null(position)) {
position <- "fill"
if (isFALSE(colours) & missing(datalabels.colour)) {
# set datalabel colour to middle gray
datalabels.colour <- "gray50"
}
p <- p + scale_rsi_colours(colours = colours)
}
if (fun_name == "portion_df"
| (fun_name == "count_df" & identical(position, "fill"))) {
# portions, so use y scale with percentage
@ -217,6 +243,9 @@ ggplot_rsi <- function(data,
if (fun_name == "count_df" & datalabels == TRUE) {
p <- p + labels_rsi_count(position = position,
x = x,
translate_ab = translate_ab,
combine_SI = combine_SI,
combine_IR = combine_IR,
datalabels.size = datalabels.size,
datalabels.colour = datalabels.colour)
}
@ -225,6 +254,12 @@ ggplot_rsi <- function(data,
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
}
@ -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]
# we work with aes_string later on
@ -296,7 +335,7 @@ facet_rsi <- function(facet = c("Interpretation", "Antibiotic"), nrow = NULL) {
stopifnot_installed_package("ggplot2")
facet <- facet[1]
facet <- facet[1]
# we work with aes_string later on
facet_deparse <- deparse(substitute(facet))
@ -331,37 +370,49 @@ scale_y_percent <- function(breaks = seq(0, 1, 0.1), limits = NULL) {
#' @rdname ggplot_rsi
#' @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")
#ggplot2::scale_fill_brewer(palette = "RdYlGn")
#ggplot2::scale_fill_manual(values = c("#b22222", "#ae9c20", "#7cfc00"))
# mixed using https://www.colorhexa.com/b22222
# and https://www.w3schools.com/colors/colors_mixer.asp
ggplot2::scale_fill_manual(values = c(S = "#22b222",
SI = "#22b222",
I = "#548022",
IR = "#b22222",
R = "#b22222"))
if (!identical(colours, FALSE)) {
original_cols <- c(S = "#61a8ff",
SI = "#61a8ff",
I = "#61f7ff",
IR = "#ff6961",
R = "#ff6961")
colours <- replace(original_cols, names(colours), colours)
ggplot2::scale_fill_manual(values = colours)
}
}
#' @rdname ggplot_rsi
#' @export
theme_rsi <- function() {
stopifnot_installed_package("ggplot2")
ggplot2::theme_minimal() +
ggplot2::theme_minimal(base_size = 10) +
ggplot2::theme(panel.grid.major.x = 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
#' @importFrom dplyr mutate %>% group_by_at
#' @export
labels_rsi_count <- function(position = NULL,
x = "Antibiotic",
translate_ab = "name",
combine_SI = TRUE,
combine_IR = FALSE,
datalabels.size = 3,
datalabels.colour = "white") {
datalabels.colour = "gray15") {
stopifnot_installed_package("ggplot2")
if (is.null(position)) {
position <- "fill"
@ -369,23 +420,24 @@ labels_rsi_count <- function(position = NULL,
if (identical(position, "fill")) {
position <- ggplot2::position_fill(vjust = 0.5, reverse = TRUE)
}
x_name <- x
ggplot2::geom_text(mapping = ggplot2::aes_string(label = "lbl",
x = x,
y = "Value"),
position = position,
data = getlbls,
inherit.aes = FALSE,
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
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@ -157,55 +157,32 @@ mo_shortname <- function(x, language = get_locale(), ...) {
Lancefield <- FALSE
}
shorten <- function(x) {
# easiest: no transformations needed
x <- mo_fullname(x, language = "en")
# shorten for the ones that have a space: shorten first word and write out second word
shorten_these <- x %like% " " & !x %like% "Streptococcus group "
x[shorten_these] <- paste0(substr(x[shorten_these], 1, 1),
". ",
x[shorten_these] %>%
strsplit(" ", fixed = TRUE) %>%
unlist() %>%
.[2])
x
}
if (isFALSE(Becker) & isFALSE(Lancefield)) {
result <- shorten(x)
} else {
# get result without transformations
res1 <- AMR::as.mo(x, Becker = FALSE, Lancefield = FALSE, reference_df = dots$reference_df)
# and result with transformations
res2 <- suppressWarnings(AMR::as.mo(res1, ...))
if (res1 == res2
& !res1 %like% "^B_STRPT_GR") {
result <- shorten(x)
} else {
res2_fullname <- mo_fullname(res2, language = language)
res2_fullname[res2_fullname %like% " \\(CoNS\\)"] <- "CoNS"
res2_fullname[res2_fullname %like% " \\(CoPS\\)"] <- "CoPS"
res2_fullname[res2_fullname %like% " \\(KNS\\)"] <- "KNS"
res2_fullname[res2_fullname %like% " \\(KPS\\)"] <- "KPS"
res2_fullname[res2_fullname %like% " \\(CNS\\)"] <- "CNS"
res2_fullname[res2_fullname %like% " \\(CPS\\)"] <- "CPS"
res2_fullname <- gsub("Streptococcus (group|Gruppe|gruppe|groep|grupo|gruppo|groupe) (.)",
"G\\2S",
res2_fullname) # turn "Streptococcus group A" and "Streptococcus grupo A" to "GAS"
res2_fullname_vector <- res2_fullname[res2_fullname == mo_fullname(res1)]
res2_fullname[res2_fullname == mo_fullname(res1)] <- paste0(substr(mo_genus(res2_fullname_vector), 1, 1),
". ",
suppressWarnings(mo_species(res2_fullname_vector)))
if (sum(res1 == res2, na.rm = TRUE) > 0) {
res1[res1 == res2] <- paste0(substr(mo_genus(res1[res1 == res2]), 1, 1),
". ",
suppressWarnings(mo_species(res1[res1 == res2])))
}
res1[res1 != res2] <- res2_fullname
result <- as.character(res1)
}
# get result without transformations
res1 <- AMR::as.mo(x, Becker = FALSE, Lancefield = FALSE, reference_df = dots$reference_df)
# and result with transformations
res2 <- suppressWarnings(AMR::as.mo(res1, ...))
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[res2_fullname %like% " \\(SCN\\)"] <- "SCN"
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)
t(result, language = language)
}

10
_pkgdown.yml
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@ -19,9 +19,12 @@
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
url: 'https://msberends.gitlab.io/AMR'
title: 'AMR (for R)'
url: 'https://msberends.gitlab.io/AMR'
development:
mode: release # improves indexing by search engines
news:
one_page: true
navbar:
title: 'AMR (for R)'
@ -177,9 +180,6 @@ authors:
Bhanu N. M. Sinha:
href: https://www.rug.nl/staff/b.sinha/
development:
mode: release # improves indexing by search engines
template:
assets: pkgdown/logos # use logos in this folder
params:

2
docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<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>
</div>

2
docs/articles/index.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<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>
</div>

2
docs/authors.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<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>
</div>

2
docs/index.html
View File

@ -42,7 +42,7 @@
</button>
<span class="navbar-brand">
<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>
</div>

9
docs/news/index.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<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>
</div>
@ -278,6 +278,12 @@
Please create an issue in one of our repositories if you want additions in this file.</li>
</ul>
</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>
<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>
<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>
</div>
<div id="other" class="section level4">

97
docs/reference/ggplot_rsi.html
View File

@ -47,7 +47,7 @@
<script src="../extra.js"></script>
<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 name="twitter:card" content="summary" />
@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<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>
</div>
@ -244,7 +244,7 @@
<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>
@ -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'>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'>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'>datalabels.colour</span> <span class='kw'>=</span> <span class='st'>"white"</span>, <span class='no'>...</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='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='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_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'>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>
<table class="ref-arguments">
@ -326,9 +331,13 @@
<th>nrow</th>
<td><p>(when using <code>facet</code>) number of rows</p></td>
</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>
<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>
<th>datalabels.size</th>
@ -338,6 +347,26 @@
<th>datalabels.colour</th>
<td><p>colour of the datalabels</p></td>
</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>
<th>...</th>
<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>
<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 />
<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>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>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>
@ -372,7 +401,7 @@
<span class='fu'>geom_rsi</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'>geom_rsi</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'>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='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>
@ -414,45 +447,45 @@
<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='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='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/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='kw'>facet</span> <span class='kw'>=</span> <span class='no'>Antibiotic</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'>x</span> <span class='kw'>=</span> <span class='st'>"Hospital"</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='st'>"Antibiotic"</span>,
<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</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.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='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='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='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='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='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='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='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='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>Antibiotic</span>,
<span class='kw'>facet</span> <span class='kw'>=</span> <span class='no'>mo</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='st'>"bug"</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='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'>subtitle</span> <span class='kw'>=</span> <span class='st'>"Only First Isolates, CoNS grouped according to Becker et al. (2014)"</span>,
<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Microorganisms"</span>)
<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</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='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.title</span> <span class='kw'>=</span> <span class='st'>"Antibiotic (Ears-Net code)"</span>)
<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

2
docs/reference/index.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<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>
</div>

81
man/ggplot_rsi.Rd
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@ -14,8 +14,11 @@ ggplot_rsi(data, position = NULL, x = "Antibiotic",
fill = "Interpretation", facet = NULL, breaks = seq(0, 1, 0.1),
limits = NULL, translate_ab = "name", combine_SI = TRUE,
combine_IR = FALSE, language = get_locale(), fun = count_df,
nrow = NULL, datalabels = FALSE, datalabels.size = 3,
datalabels.colour = "white", ...)
nrow = NULL, colours = c(S = "#61a8ff", SI = "#61a8ff", 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,
...)
geom_rsi(position = NULL, x = c("Antibiotic", "Interpretation"),
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_rsi_colours()
scale_rsi_colours(colours = c(S = "#61a8ff", SI = "#61a8ff", I =
"#61f7ff", IR = "#ff6961", R = "#ff6961"))
theme_rsi()
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{
\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{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.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}}
}
\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{
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
\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_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.
@ -103,7 +120,7 @@ ggplot(septic_patients \%>\% select(AMX, NIT, FOS, TMP, CIP)) +
geom_rsi()
# 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) +
geom_rsi() +
scale_y_percent() +
@ -130,6 +147,10 @@ septic_patients \%>\%
linetype = 2,
alpha = 0.25)
septic_patients \%>\%
select(AMX) \%>\%
ggplot_rsi(colours = c(SI = "yellow"))
# resistance of ciprofloxacine per age group
septic_patients \%>\%
mutate(first_isolate = first_isolate(.)) \%>\%
@ -146,44 +167,44 @@ septic_patients \%>\%
septic_patients \%>\%
select(AMX, NIT, FOS, TMP, CIP) \%>\%
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`):
septic_patients \%>\%
select(hospital_id, AMX, NIT, FOS, TMP, CIP) \%>\%
group_by(hospital_id) \%>\%
ggplot_rsi(x = hospital_id,
facet = Antibiotic,
nrow = 1) +
labs(title = "AMR of Anti-UTI Drugs Per Hospital",
x = "Hospital")
ggplot_rsi(x = "hospital_id",
facet = "Antibiotic",
nrow = 1,
title = "AMR of Anti-UTI Drugs Per Hospital",
x.title = "Hospital",
datalabels = FALSE)
# genuine analysis: check 2 most prevalent microorganisms
# genuine analysis: check 3 most prevalent microorganisms
septic_patients \%>\%
# create new bacterial ID's, with all CoNS under the same group (Becker et al.)
mutate(mo = as.mo(mo, Becker = TRUE)) \%>\%
# filter on top three bacterial ID's
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(first_isolate == TRUE) \%>\%
filter_first_isolate() \%>\%
# 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(mo, CXM, GEN, CIP) \%>\%
select(bug, CXM, GEN, CIP) \%>\%
# group by MO
group_by(mo) \%>\%
group_by(bug) \%>\%
# plot the thing, putting MOs on the facet
ggplot_rsi(x = Antibiotic,
facet = mo,
ggplot_rsi(x = "Antibiotic",
facet = "bug",
translate_ab = FALSE,
nrow = 1) +
labs(title = "AMR of Top Three Microorganisms In Blood Culture Isolates",
subtitle = "Only First Isolates, CoNS grouped according to Becker et al. (2014)",
x = "Microorganisms")
nrow = 1,
title = "AMR of Top Three Microorganisms In Blood Culture Isolates",
subtitle = expression(paste("Only First Isolates, CoNS grouped according to Becker ", italic("et al."), " (2014)")),
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),
units = "hours")))))
expect_output(print(freq(septic_patients$age)[,1:3]))
library(dplyr)
expect_output(septic_patients %>% select(1:2) %>% freq() %>% print())
expect_output(septic_patients %>% select(1:3) %>% freq() %>% print())