mirror of https://github.com/msberends/AMR.git
454 lines
20 KiB
R
Executable File
454 lines
20 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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#' AMR Plots with `ggplot2`
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#'
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#' Use these functions to create bar plots for AMR data analysis. All functions rely on [ggplot2][ggplot2::ggplot()] functions.
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#' @inheritSection lifecycle Maturing Lifecycle
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#' @param data a [data.frame] with column(s) of class [`rsi`] (see [as.rsi()])
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#' @param position position adjustment of bars, either `"fill"`, `"stack"` or `"dodge"`
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#' @param x variable to show on x axis, either `"antibiotic"` (default) or `"interpretation"` or a grouping variable
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#' @param fill variable to categorise using the plots legend, either `"antibiotic"` (default) or `"interpretation"` or a grouping variable
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#' @param breaks numeric vector of positions
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#' @param limits numeric vector of length two providing limits of the scale, use `NA` to refer to the existing minimum or maximum
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#' @param facet variable to split plots by, either `"interpretation"` (default) or `"antibiotic"` or a grouping variable
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#' @inheritParams proportion
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#' @param nrow (when using `facet`) number of rows
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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 `FALSE` to use default [ggplot2][ggplot2::ggplot()] colours.
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#' @param datalabels show datalabels using [labels_rsi_count()]
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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 arguments passed on to [geom_rsi()]
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#' @details At default, the names of antibiotics will be shown on the plots using [ab_name()]. This can be set with the `translate_ab` argument. See [count_df()].
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#'
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#' ## The Functions
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#' [geom_rsi()] will take any variable from the data that has an [`rsi`] class (created with [as.rsi()]) using [rsi_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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#'
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#' [facet_rsi()] creates 2d plots (at default based on S/I/R) using [ggplot2::facet_wrap()].
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#'
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#' [scale_y_percent()] transforms the y axis to a 0 to 100% range using [ggplot2::scale_y_continuous()].
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#'
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#' [scale_rsi_colours()] sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using [ggplot2::scale_fill_manual()].
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#'
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#' [theme_rsi()] is a [ggplot2 theme][[ggplot2::theme()] with minimal distraction.
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#'
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#' [labels_rsi_count()] print datalabels on the bars with percentage and amount of isolates using [ggplot2::geom_text()].
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#'
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#' [ggplot_rsi()] is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (`%>%`). See *Examples*.
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#' @rdname ggplot_rsi
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#' @export
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#' @inheritSection AMR Read more on Our Website!
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#' @examples
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#' if (require("ggplot2") & require("dplyr")) {
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#'
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#' # get antimicrobial results for drugs against a UTI:
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#' ggplot(example_isolates %>% select(AMX, NIT, FOS, TMP, CIP)) +
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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 <- example_isolates %>% 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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#' scale_rsi_colours() +
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#' labels_rsi_count() +
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#' theme_rsi()
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#'
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#' # or better yet, simplify this using the wrapper function - a single command:
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#' example_isolates %>%
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#' select(AMX, NIT, FOS, TMP, CIP) %>%
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#' ggplot_rsi()
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#'
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#' # get only proportions and no counts:
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#' example_isolates %>%
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#' select(AMX, NIT, FOS, TMP, CIP) %>%
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#' ggplot_rsi(datalabels = FALSE)
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#'
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#' # add other ggplot2 arguments as you like:
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#' example_isolates %>%
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#' select(AMX, NIT, FOS, TMP, CIP) %>%
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#' ggplot_rsi(width = 0.5,
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#' colour = "black",
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#' size = 1,
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#' linetype = 2,
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#' alpha = 0.25)
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#'
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#' example_isolates %>%
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#' select(AMX) %>%
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#' ggplot_rsi(colours = c(SI = "yellow"))
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#'
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#' }
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#'
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#' \donttest{
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#' # resistance of ciprofloxacine per age group
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#' example_isolates %>%
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#' mutate(first_isolate = first_isolate(.)) %>%
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#' filter(first_isolate == TRUE,
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#' mo == as.mo("E. coli")) %>%
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#' # age_groups() is also a function in this AMR package:
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#' group_by(age_group = age_groups(age)) %>%
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#' select(age_group,
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#' CIP) %>%
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#' ggplot_rsi(x = "age_group")
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#'
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#' # for colourblind mode, use divergent colours from the viridis package:
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#' example_isolates %>%
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#' select(AMX, NIT, FOS, TMP, CIP) %>%
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#' ggplot_rsi() +
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#' scale_fill_viridis_d()
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#' # a shorter version which also adjusts data label colours:
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#' example_isolates %>%
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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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#' example_isolates %>%
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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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#' 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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ggplot_rsi <- function(data,
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position = NULL,
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x = "antibiotic",
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fill = "interpretation",
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# params = list(),
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facet = NULL,
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breaks = seq(0, 1, 0.1),
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limits = NULL,
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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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minimum = 30,
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language = get_locale(),
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nrow = NULL,
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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 = "grey15",
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title = NULL,
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subtitle = NULL,
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caption = NULL,
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x.title = "Antimicrobial",
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y.title = "Proportion",
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...) {
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stop_ifnot_installed("ggplot2")
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meet_criteria(data, allow_class = "data.frame", contains_column_class = "rsi")
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meet_criteria(position, allow_class = "character", has_length = 1, is_in = c("fill", "stack", "dodge"), allow_NULL = TRUE)
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meet_criteria(x, allow_class = "character", has_length = 1)
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meet_criteria(fill, allow_class = "character", has_length = 1)
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meet_criteria(facet, allow_class = "character", has_length = 1, allow_NULL = TRUE)
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meet_criteria(breaks, allow_class = c("numeric", "integer"))
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meet_criteria(limits, allow_class = c("numeric", "integer"), has_length = 2, allow_NULL = TRUE, allow_NA = TRUE)
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meet_criteria(translate_ab, allow_class = c("character", "logical"), has_length = 1, allow_NA = TRUE)
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meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
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meet_criteria(combine_IR, allow_class = "logical", has_length = 1)
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meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_finite = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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meet_criteria(nrow, allow_class = c("numeric", "integer"), has_length = 1, allow_NULL = TRUE, is_positive = TRUE, is_finite = TRUE)
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meet_criteria(colours, allow_class = c("character", "logical"))
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meet_criteria(datalabels, allow_class = "logical", has_length = 1)
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meet_criteria(datalabels.size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
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meet_criteria(datalabels.colour, allow_class = "character", has_length = 1)
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meet_criteria(title, allow_class = "character", has_length = 1, allow_NULL = TRUE)
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meet_criteria(subtitle, allow_class = "character", has_length = 1, allow_NULL = TRUE)
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meet_criteria(caption, allow_class = "character", has_length = 1, allow_NULL = TRUE)
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meet_criteria(x.title, allow_class = "character", has_length = 1, allow_NULL = TRUE)
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meet_criteria(y.title, allow_class = "character", has_length = 1, allow_NULL = TRUE)
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# we work with aes_string later on
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x_deparse <- deparse(substitute(x))
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if (x_deparse != "x") {
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x <- x_deparse
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}
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if (x %like% '".*"') {
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x <- substr(x, 2, nchar(x) - 1)
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}
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facet_deparse <- deparse(substitute(facet))
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if (facet_deparse != "facet") {
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facet <- facet_deparse
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}
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if (facet %like% '".*"') {
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facet <- substr(facet, 2, nchar(facet) - 1)
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}
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if (facet %in% c("NULL", "")) {
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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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minimum = minimum, language = language,
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combine_SI = combine_SI, combine_IR = combine_IR, ...) +
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theme_rsi()
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if (fill == "interpretation") {
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# set RSI colours
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if (isFALSE(colours) & missing(datalabels.colour)) {
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# set datalabel colour to middle grey
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datalabels.colour <- "grey50"
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}
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p <- p + scale_rsi_colours(colours = colours)
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}
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if (identical(position, "fill")) {
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# proportions, so use y scale with percentage
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p <- p + scale_y_percent(breaks = breaks, limits = limits)
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}
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if (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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minimum = minimum,
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language = language,
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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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if (!is.null(facet)) {
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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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#' @rdname ggplot_rsi
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#' @export
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geom_rsi <- function(position = NULL,
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x = c("antibiotic", "interpretation"),
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fill = "interpretation",
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translate_ab = "name",
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minimum = 30,
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language = get_locale(),
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combine_SI = TRUE,
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combine_IR = FALSE,
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...) {
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x <- x[1]
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stop_ifnot_installed("ggplot2")
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stop_if(is.data.frame(position), "`position` is invalid. Did you accidentally use '%>%' instead of '+'?")
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meet_criteria(position, allow_class = "character", has_length = 1, is_in = c("fill", "stack", "dodge"), allow_NULL = TRUE)
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meet_criteria(x, allow_class = "character", has_length = 1)
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meet_criteria(fill, allow_class = "character", has_length = 1)
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meet_criteria(translate_ab, allow_class = c("character", "logical"), has_length = 1, allow_NA = TRUE)
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meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_finite = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
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meet_criteria(combine_IR, allow_class = "logical", has_length = 1)
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y <- "value"
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if (missing(position) | is.null(position)) {
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position <- "fill"
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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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# we work with aes_string later on
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x_deparse <- deparse(substitute(x))
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if (x_deparse != "x") {
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x <- x_deparse
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}
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if (x %like% '".*"') {
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x <- substr(x, 2, nchar(x) - 1)
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}
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if (tolower(x) %in% tolower(c("ab", "abx", "antibiotics"))) {
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x <- "antibiotic"
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} else if (tolower(x) %in% tolower(c("SIR", "RSI", "interpretations", "result"))) {
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x <- "interpretation"
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}
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ggplot2::layer(geom = "bar", stat = "identity", position = position,
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mapping = ggplot2::aes_string(x = x, y = y, fill = fill),
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params = list(...), data = function(x) {
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rsi_df(data = x,
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translate_ab = translate_ab,
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language = language,
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minimum = minimum,
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combine_SI = combine_SI,
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combine_IR = combine_IR)
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})
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}
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#' @rdname ggplot_rsi
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#' @export
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facet_rsi <- function(facet = c("interpretation", "antibiotic"), nrow = NULL) {
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facet <- facet[1]
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stop_ifnot_installed("ggplot2")
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meet_criteria(facet, allow_class = "character", has_length = 1)
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meet_criteria(nrow, allow_class = c("numeric", "integer"), has_length = 1, allow_NULL = TRUE, is_positive = TRUE, is_finite = TRUE)
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# we work with aes_string later on
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facet_deparse <- deparse(substitute(facet))
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if (facet_deparse != "facet") {
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facet <- facet_deparse
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}
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if (facet %like% '".*"') {
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facet <- substr(facet, 2, nchar(facet) - 1)
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}
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if (tolower(facet) %in% tolower(c("SIR", "RSI", "interpretations", "result"))) {
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facet <- "interpretation"
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} else if (tolower(facet) %in% tolower(c("ab", "abx", "antibiotics"))) {
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facet <- "antibiotic"
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}
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ggplot2::facet_wrap(facets = facet, scales = "free_x", nrow = nrow)
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}
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#' @rdname ggplot_rsi
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#' @export
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scale_y_percent <- function(breaks = seq(0, 1, 0.1), limits = NULL) {
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stop_ifnot_installed("ggplot2")
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meet_criteria(breaks, allow_class = c("numeric", "integer"))
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meet_criteria(limits, allow_class = c("numeric", "integer"), has_length = 2, allow_NULL = TRUE, allow_NA = TRUE)
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if (all(breaks[breaks != 0] > 1)) {
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breaks <- breaks / 100
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}
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ggplot2::scale_y_continuous(breaks = breaks,
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labels = percentage(breaks),
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limits = limits)
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}
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#' @rdname ggplot_rsi
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#' @export
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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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stop_ifnot_installed("ggplot2")
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meet_criteria(colours, allow_class = c("character", "logical"))
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# previous colour: palette = "RdYlGn"
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# previous colours: values = c("#b22222", "#ae9c20", "#7cfc00")
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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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stop_ifnot_installed("ggplot2")
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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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# 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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#' @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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minimum = 30,
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language = get_locale(),
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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 = "grey15") {
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stop_ifnot_installed("ggplot2")
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meet_criteria(position, allow_class = "character", has_length = 1, is_in = c("fill", "stack", "dodge"), allow_NULL = TRUE)
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meet_criteria(x, allow_class = "character", has_length = 1)
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meet_criteria(translate_ab, allow_class = c("character", "logical"), has_length = 1, allow_NA = TRUE)
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meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_finite = TRUE)
|
|
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
|
meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
|
|
meet_criteria(combine_IR, allow_class = "logical", has_length = 1)
|
|
meet_criteria(datalabels.size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
|
|
meet_criteria(datalabels.colour, allow_class = "character", has_length = 1)
|
|
|
|
if (is.null(position)) {
|
|
position <- "fill"
|
|
}
|
|
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,
|
|
inherit.aes = FALSE,
|
|
size = datalabels.size,
|
|
colour = datalabels.colour,
|
|
lineheight = 0.75,
|
|
data = function(x) {
|
|
transformed <- rsi_df(data = x,
|
|
translate_ab = translate_ab,
|
|
combine_SI = combine_SI,
|
|
combine_IR = combine_IR,
|
|
minimum = minimum,
|
|
language = language)
|
|
transformed$gr <- transformed[, x_name, drop = TRUE]
|
|
transformed %pm>%
|
|
pm_group_by(gr) %pm>%
|
|
pm_mutate(lbl = paste0("n=", isolates)) %pm>%
|
|
pm_ungroup() %pm>%
|
|
pm_select(-gr)
|
|
})
|
|
}
|