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AMR
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ggplot2_rsi fix

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dr. M.S. (Matthijs) Berends 2018-09-13 14:48:34 +02:00
parent cb0d74a4f0
commit d049ec9e69
3 changed files with 77 additions and 34 deletions
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74
R/ggplot_rsi.R
View File

@ -20,7 +20,7 @@
#'
#' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \code{\link[ggplot2]{ggplot}} 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{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"} (default when \code{fun} is \code{\link{count_df}})
#' @param position position adjustment of bars, either \code{"fill"}, \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"} (default when \code{fun} is \code{\link{count_df}})
#' @param x variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable
#' @param fill variable to categorise using the plots legend, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable
#' @param facet variable to split plots by, either \code{"Interpretation"} (default) or \code{"Antibiotic"} or a grouping variable
@ -56,7 +56,6 @@
#' df <- septic_patients[, c("amox", "nitr", "fosf", "trim", "cipr")]
#' ggplot(df) +
#' geom_rsi() +
#' facet_rsi() +
#' scale_y_percent() +
#' scale_rsi_colours() +
#' theme_rsi()
@ -87,12 +86,12 @@
#' ggplot_rsi() + scale_fill_viridis_d()
#'
#'
#' # it also supports groups (don't forget to use the group on `x` or `facet`):
#' # it also supports groups (don't forget to use the group var on `x` or `facet`):
#' septic_patients %>%
#' select(hospital_id, amox, nitr, fosf, trim, cipr) %>%
#' group_by(hospital_id) %>%
#' ggplot_rsi(x = "hospital_id",
#' facet = "Antibiotic",
#' ggplot_rsi(x = hospital_id,
#' facet = Antibiotic,
#' nrow = 1) +
#' labs(title = "AMR of Anti-UTI Drugs Per Hospital",
#' x = "Hospital")
@ -101,8 +100,8 @@
#' 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 2 bacterial ID's
#' filter(mo %in% top_freq(freq(.$mo), 2)) %>%
#' # filter on top three bacterial ID's
#' filter(mo %in% top_freq(freq(.$mo), 3)) %>%
#' # determine first isolates
#' mutate(first_isolate = first_isolate(.,
#' col_date = "date",
@ -110,17 +109,18 @@
#' col_mo = "mo")) %>%
#' # filter on first isolates
#' filter(first_isolate == TRUE) %>%
#' # join the `microorganisms` data set
#' left_join_microorganisms() %>%
#' # select full name and some antiseptic drugs
#' select(mo = fullname,
#' cfur, gent, cipr) %>%
#' # get short MO names (like "E. coli")
#' mutate(mo = mo_shortname(mo, Becker = TRUE)) %>%
#' # select this short name and some antiseptic drugs
#' select(mo, cfur, gent, cipr) %>%
#' # group by MO
#' group_by(mo) %>%
#' # plot the thing, putting MOs on the facet
#' ggplot_rsi(x = "Antibiotic",
#' facet = "mo") +
#' labs(title = "AMR of Top Two Microorganisms In Blood Culture Isolates",
#' ggplot_rsi(x = Antibiotic,
#' facet = mo,
#' 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")
#' }
@ -144,6 +144,28 @@ ggplot_rsi <- function(data,
stop("`fun` must be portion_df or count_df")
}
x <- x[1]
facet <- facet[1]
# we work with aes_string later on
x_deparse <- deparse(substitute(x))
if (x_deparse != "x") {
x <- x_deparse
}
if (x %like% '".*"') {
x <- substr(x, 2, nchar(x) - 1)
}
facet_deparse <- deparse(substitute(facet))
if (facet_deparse != "facet") {
facet <- facet_deparse
}
if (facet %like% '".*"') {
facet <- substr(facet, 2, nchar(facet) - 1)
}
if (facet %in% c("NULL", "")) {
facet <- NULL
}
p <- ggplot2::ggplot(data = data) +
geom_rsi(position = position, x = x, fill = fill, translate_ab = translate_ab, fun = fun, ...) +
theme_rsi()
@ -190,6 +212,16 @@ geom_rsi <- function(position = NULL,
}
x <- x[1]
# we work with aes_string later on
x_deparse <- deparse(substitute(x))
if (x_deparse != "x") {
x <- x_deparse
}
if (x %like% '".*"') {
x <- substr(x, 2, nchar(x) - 1)
}
if (tolower(x) %in% tolower(c('ab', 'antibiotic', 'abx', 'antibiotics'))) {
x <- "Antibiotic"
} else if (tolower(x) %in% tolower(c('SIR', 'RSI', 'interpretation', 'interpretations', 'result'))) {
@ -208,7 +240,17 @@ geom_rsi <- function(position = NULL,
#' @export
facet_rsi <- function(facet = c("Interpretation", "Antibiotic"), nrow = NULL) {
facet <- facet[1]
facet <- facet[1]
# we work with aes_string later on
facet_deparse <- deparse(substitute(facet))
if (facet_deparse != "facet") {
facet <- facet_deparse
}
if (facet %like% '".*"') {
facet <- substr(facet, 2, nchar(facet) - 1)
}
if (tolower(facet) %in% tolower(c('SIR', 'RSI', 'interpretation', 'interpretations', 'result'))) {
facet <- "Interpretation"
} else if (tolower(facet) %in% tolower(c('ab', 'antibiotic', 'abx', 'antibiotics'))) {

7
R/mo_property.R
View File

@ -142,12 +142,13 @@ mo_shortname <- function(x, Becker = FALSE, Lancefield = FALSE, language = NULL)
res2_fullname <- mo_fullname(res2)
res2_fullname[res2_fullname %like% "\\(CoNS\\)"] <- "CoNS"
res2_fullname[res2_fullname %like% "\\(CoPS\\)"] <- "CoPS"
res2_fullname <- gsub("Streptococcus (group|gruppe|Gruppe|groep|grupo) (.)",
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[res2_fullname == mo_fullname(x)] <- paste0(substr(mo_genus(res2_fullname), 1, 1),
res2_fullname_vector <- res2_fullname[res2_fullname == mo_fullname(x)]
res2_fullname[res2_fullname == mo_fullname(x)] <- paste0(substr(mo_genus(res2_fullname_vector), 1, 1),
". ",
suppressWarnings(mo_species(res2_fullname)))
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),
". ",

30
man/ggplot_rsi.Rd
View File

@ -28,7 +28,7 @@ theme_rsi()
\arguments{
\item{data}{a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}})}
\item{position}{position adjustment of bars, either \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"} (default when \code{fun} is \code{\link{count_df}})}
\item{position}{position adjustment of bars, either \code{"fill"}, \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"} (default when \code{fun} is \code{\link{count_df}})}
\item{x}{variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable}
@ -75,7 +75,6 @@ ggplot(septic_patients \%>\% select(amox, nitr, fosf, trim, cipr)) +
df <- septic_patients[, c("amox", "nitr", "fosf", "trim", "cipr")]
ggplot(df) +
geom_rsi() +
facet_rsi() +
scale_y_percent() +
scale_rsi_colours() +
theme_rsi()
@ -106,12 +105,12 @@ septic_patients \%>\%
ggplot_rsi() + scale_fill_viridis_d()
# it also supports groups (don't forget to use the group on `x` or `facet`):
# it also supports groups (don't forget to use the group var on `x` or `facet`):
septic_patients \%>\%
select(hospital_id, amox, nitr, fosf, trim, cipr) \%>\%
group_by(hospital_id) \%>\%
ggplot_rsi(x = "hospital_id",
facet = "Antibiotic",
ggplot_rsi(x = hospital_id,
facet = Antibiotic,
nrow = 1) +
labs(title = "AMR of Anti-UTI Drugs Per Hospital",
x = "Hospital")
@ -120,8 +119,8 @@ septic_patients \%>\%
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 2 bacterial ID's
filter(mo \%in\% top_freq(freq(.$mo), 2)) \%>\%
# filter on top three bacterial ID's
filter(mo \%in\% top_freq(freq(.$mo), 3)) \%>\%
# determine first isolates
mutate(first_isolate = first_isolate(.,
col_date = "date",
@ -129,17 +128,18 @@ septic_patients \%>\%
col_mo = "mo")) \%>\%
# filter on first isolates
filter(first_isolate == TRUE) \%>\%
# join the `microorganisms` data set
left_join_microorganisms() \%>\%
# select full name and some antiseptic drugs
select(mo = fullname,
cfur, gent, cipr) \%>\%
# get short MO names (like "E. coli")
mutate(mo = mo_shortname(mo, Becker = TRUE)) \%>\%
# select this short name and some antiseptic drugs
select(mo, cfur, gent, cipr) \%>\%
# group by MO
group_by(mo) \%>\%
# plot the thing, putting MOs on the facet
ggplot_rsi(x = "Antibiotic",
facet = "mo") +
labs(title = "AMR of Top Two Microorganisms In Blood Culture Isolates",
ggplot_rsi(x = Antibiotic,
facet = mo,
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")
}