mirror of
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(v0.6.1.9046) ggplot fix
This commit is contained in:
20
R/age.R
20
R/age.R
@ -47,8 +47,8 @@ age <- function(x, reference = Sys.Date(), exact = FALSE) {
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stop("`x` and `reference` must be of same length, or `reference` must be of length 1.")
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}
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}
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x <- base::as.POSIXlt(x)
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reference <- base::as.POSIXlt(reference)
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x <- as.POSIXlt(x)
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reference <- as.POSIXlt(reference)
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# from https://stackoverflow.com/a/25450756/4575331
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years_gap <- reference$year - x$year
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@ -59,13 +59,17 @@ age <- function(x, reference = Sys.Date(), exact = FALSE) {
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# add decimals
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if (exact == TRUE) {
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# get dates of `x` when `x` would have the year of `reference`
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x_in_reference_year <- base::as.POSIXlt(paste0(format(reference, "%Y"), format(x, "-%m-%d")))
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x_in_reference_year <- as.POSIXlt(paste0(format(reference, "%Y"), format(x, "-%m-%d")))
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# get differences in days
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n_days_x_rest <- base::as.double(base::difftime(reference, x_in_reference_year, units = "days"))
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n_days_x_rest <- as.double(difftime(reference, x_in_reference_year, units = "days"))
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# get numbers of days the years of `reference` has for a reliable denominator
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n_days_reference_year <- base::as.POSIXlt(paste0(format(reference, "%Y"), "-12-31"))$yday + 1
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n_days_reference_year <- as.POSIXlt(paste0(format(reference, "%Y"), "-12-31"))$yday + 1
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# add decimal parts of year
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ages <- ages + (n_days_x_rest / n_days_reference_year)
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mod <- n_days_x_rest / n_days_reference_year
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# negative mods are cases where `x_in_reference_year` > `reference` - so 'add' a year
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mod[mod < 0] <- 1 + mod[mod < 0]
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# and finally add to ages
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ages <- ages + mod
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}
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if (any(ages < 0, na.rm = TRUE)) {
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@ -79,10 +83,6 @@ age <- function(x, reference = Sys.Date(), exact = FALSE) {
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ages
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}
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age_to_toDate <- function(age) {
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}
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#' Split ages into age groups
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#'
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#' Split ages into age groups defined by the \code{split} parameter. This allows for easier demographic (antimicrobial resistance) analysis.
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170
R/ggplot_rsi.R
170
R/ggplot_rsi.R
@ -21,7 +21,7 @@
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#' AMR plots with \code{ggplot2}
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#'
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#' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \code{\link[ggplot2]{ggplot}} functions.
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#' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \code{\link[ggplot2]{ggplot}2} functions.
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#' @param data a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}})
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#' @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"}
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#' @param x variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable
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@ -32,11 +32,17 @@
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#' @param fun function to transform \code{data}, either \code{\link{count_df}} (default) or \code{\link{portion_df}}
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#' @inheritParams portion
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#' @param nrow (when using \code{facet}) number of rows
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#' @param datalabels show datalabels using \code{labels_rsi_count}, will at default only be shown when \code{fun = count_df}
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#' @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.
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#' @param datalabels show datalabels using \code{labels_rsi_count}, will only be shown when \code{fun = count_df}
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#' @param datalabels.size size of the datalabels
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#' @param datalabels.colour colour of the datalabels
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#' @param title text to show as title of the plot
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#' @param subtitle text to show as subtitle of the plot
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#' @param caption text to show as caption of the plot
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#' @param x.title text to show as x axis description
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#' @param y.title text to show as y axis description
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#' @param ... other parameters passed on to \code{geom_rsi}
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#' @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)}.
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#' @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}}.
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#'
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#' \strong{The functions}\cr
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#' \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.
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@ -45,7 +51,7 @@
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#'
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#' \code{scale_y_percent} transforms the y axis to a 0 to 100\% range using \code{\link[ggplot2]{scale_continuous}}.
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#'
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#' \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}}.
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#' \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}}.
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#'
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#' \code{theme_rsi} is a \code{ggplot \link[ggplot2]{theme}} with minimal distraction.
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#'
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@ -65,7 +71,7 @@
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#' geom_rsi()
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#'
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#' # prettify the plot using some additional functions:
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#' df <- septic_patients[, c("AMX", "NIT", "FOS", "TMP", "CIP")]
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#' df <- septic_patients %>% select(AMX, NIT, FOS, TMP, CIP)
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#' ggplot(df) +
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#' geom_rsi() +
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#' scale_y_percent() +
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@ -92,6 +98,10 @@
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#' linetype = 2,
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#' alpha = 0.25)
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#'
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#' septic_patients %>%
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#' select(AMX) %>%
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#' ggplot_rsi(colours = c(SI = "yellow"))
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#'
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#' # resistance of ciprofloxacine per age group
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#' septic_patients %>%
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#' mutate(first_isolate = first_isolate(.)) %>%
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@ -108,45 +118,45 @@
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#' septic_patients %>%
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#' select(AMX, NIT, FOS, TMP, CIP) %>%
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#' ggplot_rsi() + scale_fill_viridis_d()
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#' # a shorter version which also adjusts data label colours:
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#' septic_patients %>%
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#' select(AMX, NIT, FOS, TMP, CIP) %>%
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#' ggplot_rsi(colours = FALSE)
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#'
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#'
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#' # it also supports groups (don't forget to use the group var on `x` or `facet`):
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#' septic_patients %>%
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#' select(hospital_id, AMX, NIT, FOS, TMP, CIP) %>%
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#' group_by(hospital_id) %>%
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#' ggplot_rsi(x = hospital_id,
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#' facet = Antibiotic,
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#' nrow = 1) +
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#' labs(title = "AMR of Anti-UTI Drugs Per Hospital",
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#' x = "Hospital")
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#' ggplot_rsi(x = "hospital_id",
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#' facet = "Antibiotic",
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#' nrow = 1,
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#' title = "AMR of Anti-UTI Drugs Per Hospital",
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#' x.title = "Hospital",
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#' datalabels = FALSE)
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#'
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#' # genuine analysis: check 2 most prevalent microorganisms
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#' # genuine analysis: check 3 most prevalent microorganisms
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#' septic_patients %>%
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#' # create new bacterial ID's, with all CoNS under the same group (Becker et al.)
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#' mutate(mo = as.mo(mo, Becker = TRUE)) %>%
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#' # filter on top three bacterial ID's
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#' filter(mo %in% top_freq(freq(.$mo), 3)) %>%
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#' # determine first isolates
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#' mutate(first_isolate = first_isolate(.,
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#' col_date = "date",
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#' col_patient_id = "patient_id",
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#' col_mo = "mo")) %>%
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#' # filter on first isolates
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#' filter(first_isolate == TRUE) %>%
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#' filter_first_isolate() %>%
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#' # get short MO names (like "E. coli")
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#' mutate(mo = mo_shortname(mo, Becker = TRUE)) %>%
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#' mutate(bug = mo_shortname(mo, Becker = TRUE)) %>%
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#' # select this short name and some antiseptic drugs
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#' select(mo, CXM, GEN, CIP) %>%
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#' select(bug, CXM, GEN, CIP) %>%
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#' # group by MO
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#' group_by(mo) %>%
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#' group_by(bug) %>%
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#' # plot the thing, putting MOs on the facet
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#' ggplot_rsi(x = Antibiotic,
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#' facet = mo,
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#' ggplot_rsi(x = "Antibiotic",
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#' facet = "bug",
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#' translate_ab = FALSE,
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#' nrow = 1) +
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#' labs(title = "AMR of Top Three Microorganisms In Blood Culture Isolates",
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#' subtitle = "Only First Isolates, CoNS grouped according to Becker et al. (2014)",
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#' x = "Microorganisms")
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#' nrow = 1,
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#' title = "AMR of Top Three Microorganisms In Blood Culture Isolates",
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#' subtitle = expression(paste("Only First Isolates, CoNS grouped according to Becker ", italic("et al."), " (2014)")),
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#' x.title = "Antibiotic (EARS-Net code)")
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#' }
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ggplot_rsi <- function(data,
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position = NULL,
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@ -162,9 +172,19 @@ ggplot_rsi <- function(data,
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language = get_locale(),
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fun = count_df,
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nrow = NULL,
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datalabels = FALSE,
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datalabels.size = 3,
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datalabels.colour = "white",
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colours = c(S = "#61a8ff",
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SI = "#61a8ff",
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I = "#61f7ff",
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IR = "#ff6961",
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R = "#ff6961"),
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datalabels = TRUE,
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datalabels.size = 2.5,
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datalabels.colour = "gray15",
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title = NULL,
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subtitle = NULL,
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caption = NULL,
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x.title = NULL,
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y.title = NULL,
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...) {
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stopifnot_installed_package("ggplot2")
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@ -196,6 +216,10 @@ ggplot_rsi <- function(data,
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facet <- NULL
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}
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if (is.null(position)) {
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position <- "fill"
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}
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p <- ggplot2::ggplot(data = data) +
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geom_rsi(position = position, x = x, fill = fill, translate_ab = translate_ab,
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fun = fun, combine_SI = combine_SI, combine_IR = combine_IR, ...) +
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@ -203,11 +227,13 @@ ggplot_rsi <- function(data,
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if (fill == "Interpretation") {
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# set RSI colours
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p <- p + scale_rsi_colours()
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}
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if (is.null(position)) {
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position <- "fill"
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if (isFALSE(colours) & missing(datalabels.colour)) {
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# set datalabel colour to middle gray
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datalabels.colour <- "gray50"
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}
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p <- p + scale_rsi_colours(colours = colours)
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}
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if (fun_name == "portion_df"
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# portions, so use y scale with percentage
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@ -217,6 +243,9 @@ ggplot_rsi <- function(data,
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if (fun_name == "count_df" & datalabels == TRUE) {
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p <- p + labels_rsi_count(position = position,
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x = x,
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translate_ab = translate_ab,
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combine_SI = combine_SI,
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combine_IR = combine_IR,
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datalabels.size = datalabels.size,
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datalabels.colour = datalabels.colour)
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}
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@ -225,6 +254,12 @@ ggplot_rsi <- function(data,
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p <- p + facet_rsi(facet = facet, nrow = nrow)
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}
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p <- p + ggplot2::labs(title = title,
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subtitle = subtitle,
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caption = caption,
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x = x.title,
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y = y.title)
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p
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}
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@ -261,6 +296,10 @@ geom_rsi <- function(position = NULL,
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}
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}
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if (identical(position, "fill")) {
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position <- ggplot2::position_fill(vjust = 0.5, reverse = TRUE)
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}
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x <- x[1]
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# we work with aes_string later on
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@ -296,7 +335,7 @@ facet_rsi <- function(facet = c("Interpretation", "Antibiotic"), nrow = NULL) {
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stopifnot_installed_package("ggplot2")
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facet <- facet[1]
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facet <- facet[1]
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# we work with aes_string later on
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facet_deparse <- deparse(substitute(facet))
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@ -331,37 +370,49 @@ scale_y_percent <- function(breaks = seq(0, 1, 0.1), limits = NULL) {
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#' @rdname ggplot_rsi
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#' @export
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scale_rsi_colours <- function() {
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scale_rsi_colours <- function(colours = c(S = "#61a8ff",
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SI = "#61a8ff",
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I = "#61f7ff",
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IR = "#ff6961",
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R = "#ff6961")) {
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stopifnot_installed_package("ggplot2")
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#ggplot2::scale_fill_brewer(palette = "RdYlGn")
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#ggplot2::scale_fill_manual(values = c("#b22222", "#ae9c20", "#7cfc00"))
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# mixed using https://www.colorhexa.com/b22222
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# and https://www.w3schools.com/colors/colors_mixer.asp
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ggplot2::scale_fill_manual(values = c(S = "#22b222",
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SI = "#22b222",
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I = "#548022",
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IR = "#b22222",
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R = "#b22222"))
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if (!identical(colours, FALSE)) {
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original_cols <- c(S = "#61a8ff",
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SI = "#61a8ff",
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I = "#61f7ff",
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IR = "#ff6961",
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R = "#ff6961")
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colours <- replace(original_cols, names(colours), colours)
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ggplot2::scale_fill_manual(values = colours)
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}
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}
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#' @rdname ggplot_rsi
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#' @export
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theme_rsi <- function() {
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stopifnot_installed_package("ggplot2")
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ggplot2::theme_minimal() +
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ggplot2::theme_minimal(base_size = 10) +
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ggplot2::theme(panel.grid.major.x = ggplot2::element_blank(),
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panel.grid.minor = ggplot2::element_blank(),
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panel.grid.major.y = ggplot2::element_line(colour = "grey75"))
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panel.grid.major.y = ggplot2::element_line(colour = "grey75"),
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# center title and subtitle
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plot.title = ggplot2::element_text(hjust = 0.5),
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plot.subtitle = ggplot2::element_text(hjust = 0.5))
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}
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#' @rdname ggplot_rsi
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#' @importFrom dplyr mutate %>% group_by_at
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#' @export
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labels_rsi_count <- function(position = NULL,
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x = "Antibiotic",
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translate_ab = "name",
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combine_SI = TRUE,
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combine_IR = FALSE,
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datalabels.size = 3,
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datalabels.colour = "white") {
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datalabels.colour = "gray15") {
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stopifnot_installed_package("ggplot2")
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if (is.null(position)) {
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position <- "fill"
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@ -369,23 +420,24 @@ labels_rsi_count <- function(position = NULL,
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if (identical(position, "fill")) {
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position <- ggplot2::position_fill(vjust = 0.5, reverse = TRUE)
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}
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x_name <- x
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ggplot2::geom_text(mapping = ggplot2::aes_string(label = "lbl",
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x = x,
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y = "Value"),
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position = position,
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data = getlbls,
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inherit.aes = FALSE,
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size = datalabels.size,
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colour = datalabels.colour)
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colour = datalabels.colour,
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lineheight = 0.75,
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data = function(x) {
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# labels are only shown when function is count_df,
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# so no need parameterise it here
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count_df(data = x,
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translate_ab = translate_ab,
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combine_SI = combine_SI,
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combine_IR = combine_IR) %>%
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group_by_at(x_name) %>%
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mutate(lbl = paste0(percent(Value / sum(Value, na.rm = TRUE), force_zero = TRUE),
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"\n(n=", Value, ")"))
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})
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}
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#' @importFrom dplyr %>% group_by mutate
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getlbls <- function(data) {
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data %>%
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count_df() %>%
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group_by(Antibiotic) %>%
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mutate(lbl = paste0(percent(Value / sum(Value, na.rm = TRUE), force_zero = TRUE),
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" (n=", Value, ")")) %>%
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mutate(lbl = ifelse(lbl == "0.0% (n=0)", "", lbl))
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}
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@ -157,55 +157,32 @@ mo_shortname <- function(x, language = get_locale(), ...) {
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Lancefield <- FALSE
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}
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shorten <- function(x) {
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# easiest: no transformations needed
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x <- mo_fullname(x, language = "en")
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# shorten for the ones that have a space: shorten first word and write out second word
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shorten_these <- x %like% " " & !x %like% "Streptococcus group "
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x[shorten_these] <- paste0(substr(x[shorten_these], 1, 1),
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". ",
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x[shorten_these] %>%
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strsplit(" ", fixed = TRUE) %>%
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unlist() %>%
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.[2])
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x
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}
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if (isFALSE(Becker) & isFALSE(Lancefield)) {
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result <- shorten(x)
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} else {
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# get result without transformations
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res1 <- AMR::as.mo(x, Becker = FALSE, Lancefield = FALSE, reference_df = dots$reference_df)
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# and result with transformations
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res2 <- suppressWarnings(AMR::as.mo(res1, ...))
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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)
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user