# ==================================================================== # # TITLE: # # AMR: An R Package for Working with Antimicrobial Resistance Data # # # # SOURCE CODE: # # https://github.com/msberends/AMR # # # # PLEASE CITE THIS SOFTWARE AS: # # Berends MS, Luz CF, Friedrich AW, et al. (2022). # # AMR: An R Package for Working with Antimicrobial Resistance Data. # # Journal of Statistical Software, 104(3), 1-31. # # https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # # colleagues from around the world, see our website. # # # # This R package is free software; you can freely use and distribute # # it for both personal and commercial purposes under the terms of the # # GNU General Public License version 2.0 (GNU GPL-2), as published by # # the Free Software Foundation. # # We created this package for both routine data analysis and academic # # research and it was publicly released in the hope that it will be # # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # # # # Visit our website for the full manual and a complete tutorial about # # how to conduct AMR data analysis: https://amr-for-r.org # # ==================================================================== # test_that("test-plotting.R", { skip_on_cran() if (AMR:::pkg_is_available("ggplot2", also_load = TRUE)) { pdf(NULL) # prevent Rplots.pdf being created # scale_*_mic aesthetics <- c("x", "y", "colour", "fill") expected_methods <- c("transform", "transform_df", "breaks", "labels", "limits") for (aest in aesthetics) { scale_fn_name <- paste0("scale_", aest, "_continuous") scale_obj <- getExportedValue("ggplot2", scale_fn_name)() for (method in expected_methods) { expect_true(is.function(scale_obj[[method]]) || method %in% names(scale_obj), info = paste0("Method '", method, "' is missing in ggplot2::", scale_fn_name) ) } } # scale_*_sir aesthetics <- c("colour", "fill") expected_methods <- c("transform", "transform_df", "labels", "limits") for (aest in aesthetics) { scale_fn_name <- "scale_discrete_manual" scale_obj <- getExportedValue("ggplot2", scale_fn_name)(aesthetics = aest) for (method in expected_methods) { expect_true(is.function(scale_obj[[method]]) || method %in% names(scale_obj), info = paste0("Method '", method, "' is missing in ggplot2::", scale_fn_name) ) } } for (method in expected_methods) { expect_true(is.function(ggplot2::scale_x_discrete()[[method]]) || method %in% names(ggplot2::scale_x_discrete()), info = paste0("Method '", method, "' is missing in ggplot2::", "scale_x_discrete") ) } expect_inherits( ggplot( data.frame( count = c(1, 2, 3, 4), sir = c("S", "I", "R", "SDD") ), aes(x = sir, y = count, fill = sir) ) + geom_col() + scale_x_sir(eucast_I = F, language = "el") + scale_fill_sir(eucast_I = T, language = "nl"), "gg" ) expect_inherits( ggplot( data.frame( mic = as.mic(c(2, 4, 8, 16)), sir = as.sir(c("S", "I", "R", "SDD")) ), aes(x = sir, y = mic) ) + geom_point() + scale_y_mic(), "gg" ) expect_inherits( ggplot( data.frame( mic = as.mic(c(2, 4, 8, 16)), sir = as.sir(c("S", "I", "R", "SDD")) ), aes(x = sir, y = mic) ) + geom_col() + scale_y_mic(), "gg" ) expect_inherits( ggplot( data.frame( mic = as.mic(c(2, 4, 8, 16)), sir = as.sir(c("S", "I", "R", "SDD")) ), aes(x = sir, y = mic) ) + geom_col() + scale_y_mic(mic_range = c(4, 16)) + scale_x_sir(), "gg" ) } })