From 671d657fd803292db5596dd536d2e9785a896c22 Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Tue, 18 Feb 2025 08:07:02 +0100 Subject: [PATCH] (v2.1.1.9152) MIC plot fix --- DESCRIPTION | 4 +-- NEWS.md | 3 +- PythonPackage/AMR/AMR.egg-info/PKG-INFO | 2 +- ...ny.whl => AMR-2.1.1.9152-py3-none-any.whl} | Bin 10253 -> 10252 bytes PythonPackage/AMR/dist/amr-2.1.1.9151.tar.gz | Bin 10061 -> 0 bytes PythonPackage/AMR/dist/amr-2.1.1.9152.tar.gz | Bin 0 -> 10063 bytes PythonPackage/AMR/setup.py | 2 +- R/mic.R | 28 ++++++++++++------ R/plotting.R | 25 ++++++++++++---- ....txt => gpt_training_text_v2.1.1.9152.txt} | 2 +- tests/testthat/test-mic.R | 7 +++-- 11 files changed, 50 insertions(+), 23 deletions(-) rename PythonPackage/AMR/dist/{AMR-2.1.1.9151-py3-none-any.whl => AMR-2.1.1.9152-py3-none-any.whl} (84%) delete mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9151.tar.gz create mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9152.tar.gz rename data-raw/{gpt_training_text_v2.1.1.9151.txt => gpt_training_text_v2.1.1.9152.txt} (99%) diff --git a/DESCRIPTION b/DESCRIPTION index 035f7d6ff..f1a26672e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 2.1.1.9151 -Date: 2025-02-15 +Version: 2.1.1.9152 +Date: 2025-02-18 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by diff --git a/NEWS.md b/NEWS.md index 86fdc3319..09a85a9ee 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9151 +# AMR 2.1.1.9152 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)* @@ -64,6 +64,7 @@ This package now supports not only tools for AMR data analysis in clinical setti * Added Tigemonam (`TNM`), a monobactam * MICs * Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960) + * Fixed a bug in `as.mic()` that failed translation of scientifically formatted numbers * Added new argument `keep_operators` to `as.mic()`. This can be `"all"` (default), `"none"`, or `"edges"`. This argument is also available in the new `rescale_mic()` and `scale_*_mic()` functions. * Comparisons of MIC values are now more strict. For example, `>32` is higher than (and never equal to) `32`. Thus, `as.mic(">32") == as.mic(32)` now returns `FALSE`, and `as.mic(">32") > as.mic(32)` now returns `TRUE`. * Sorting of MIC values (using `sort()`) was fixed in the same manner; `<0.001` now gets sorted before `0.001`, and `>0.001` gets sorted after `0.001`. diff --git a/PythonPackage/AMR/AMR.egg-info/PKG-INFO b/PythonPackage/AMR/AMR.egg-info/PKG-INFO index a63234a6d..ca7676eda 100644 --- a/PythonPackage/AMR/AMR.egg-info/PKG-INFO +++ b/PythonPackage/AMR/AMR.egg-info/PKG-INFO @@ -1,6 +1,6 @@ Metadata-Version: 2.2 Name: AMR -Version: 2.1.1.9151 +Version: 2.1.1.9152 Summary: A Python wrapper for the AMR R package Home-page: https://github.com/msberends/AMR Author: Matthijs Berends diff --git a/PythonPackage/AMR/dist/AMR-2.1.1.9151-py3-none-any.whl b/PythonPackage/AMR/dist/AMR-2.1.1.9152-py3-none-any.whl similarity index 84% rename from PythonPackage/AMR/dist/AMR-2.1.1.9151-py3-none-any.whl rename to PythonPackage/AMR/dist/AMR-2.1.1.9152-py3-none-any.whl index 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lDm?yCuV#9plhrX_#`&dE_5V)IuOTpa%~mFVxGi|N{{RXB)8YUC literal 0 HcmV?d00001 diff --git a/PythonPackage/AMR/setup.py b/PythonPackage/AMR/setup.py index c3bbccec7..a60ede2b5 100644 --- a/PythonPackage/AMR/setup.py +++ b/PythonPackage/AMR/setup.py @@ -2,7 +2,7 @@ from setuptools import setup, find_packages setup( name='AMR', - version='2.1.1.9151', + version='2.1.1.9152', packages=find_packages(), install_requires=[ 'rpy2', diff --git a/R/mic.R b/R/mic.R index e19aa9c9d..bc37f2f86 100644 --- a/R/mic.R +++ b/R/mic.R @@ -43,9 +43,14 @@ VALID_MIC_LEVELS <- c(t(vapply(FUN.VALUE = character(length(VALID_MIC_LEVELS)), c("<", "<=", "", ">=", ">"), paste0, VALID_MIC_LEVELS))) -COMMON_MIC_VALUES <- c(0.001, 0.002, 0.004, 0.008, 0.016, 0.032, 0.064, - 0.125, 0.25, 0.5, 1, 2, 4, 8, 16, 32, - 64, 128, 256, 512, 1024) +COMMON_MIC_VALUES <- c(0.0001, 0.0002, 0.0005, + 0.001, 0.002, 0.004, 0.008, + 0.016, 0.032, 0.064, + 0.125, 0.25, 0.5, + 1, 2, 4, 8, + 16, 32, 64, + 128, 256, 512, + 1024, 2048, 4096) #' Transform Input to Minimum Inhibitory Concentrations (MIC) #' @@ -158,7 +163,7 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all") { if (is.mic(x) && (keep_operators == "all" || !any(x %like% "[>=<]", na.rm = TRUE))) { if (!identical(levels(x), VALID_MIC_LEVELS)) { - # from an older AMR version - just update MIC factor levels + # might be from an older AMR version - just update MIC factor levels x <- set_clean_class(factor(as.character(x), levels = VALID_MIC_LEVELS, ordered = TRUE), new_class = c("mic", "ordered", "factor")) } @@ -184,20 +189,19 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all") { # comma to period x <- gsub(",", ".", x, fixed = TRUE) - # transform scientific notation - x[x %like% "[-]?[0-9]+([.][0-9]+)?e[-]?[0-9]+"] <- as.double(x[x %like% "[-]?[0-9]+([.][0-9]+)?e[-]?[0-9]+"]) # transform Unicode for >= and <= x <- gsub("\u2264", "<=", x, fixed = TRUE) x <- gsub("\u2265", ">=", x, fixed = TRUE) # remove other invalid characters - x <- gsub("[^a-zA-Z0-9.><= ]+", "", x, perl = TRUE) - # remove space between operator and number ("<= 0.002" -> "<=0.002") - x <- gsub("(<|=|>) +", "\\1", x, perl = TRUE) + x <- gsub("[^a-zA-Z0-9.><= -]+", "", x, perl = TRUE) # transform => to >= and =< to <= x <- gsub("=<", "<=", x, fixed = TRUE) x <- gsub("=>", ">=", x, fixed = TRUE) # Remove leading == and = x <- gsub("^=+", "", x) + # retrieve signs and remove them from input + x_signs <- trimws(gsub("[^>=<]", "", x)) + x <- trimws(gsub("[>=<]", "", x)) # dots without a leading zero must start with 0 x <- gsub("([^0-9]|^)[.]", "\\10.", x, perl = TRUE) # values like "<=0.2560.512" should be 0.512 @@ -217,6 +221,12 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all") { x[x %like% "[.]"] <- gsub("0+$", "", x[x %like% "[.]"]) # never end with dot x <- gsub("[.]$", "", x, perl = TRUE) + # remove scientific notation + x[x %like% "[0-9]e[-]?[0-9]"] <- trimws(format(suppressWarnings(as.double(x[x %like% "[0-9]e[-]?[0-9]"])), scientific = FALSE)) + # add signs again + x <- paste0(x_signs, x) + # remove NAs introduced by format() + x <- gsub("(NA)+", "", x) # trim it x <- trimws2(x) diff --git a/R/plotting.R b/R/plotting.R index 775ed96f7..7c50b93f8 100755 --- a/R/plotting.R +++ b/R/plotting.R @@ -237,20 +237,33 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) { "In `scale_", aest, "_mic()`, `limits` cannot be combined with `mic_range`, as they working identically. Use `mic_range` OR `limits`.", call = FALSE) mic_range <- args$limits } - # do not take these arguments into account, as they will be overwritten and seem to allow weird behaviour + # do not take these arguments into account, as they will be overwritten and seem to allow weird behaviour if set anyway args[c("aesthetics", "trans", "transform", "transform_df", "breaks", "labels", "limits")] <- NULL scale <- do.call(ggplot_fn, args) scale$transform <- function(x) { - as.double(rescale_mic(x = as.double(x), keep_operators = , "labels", mic_range = mic_range, as.mic = TRUE)) + as.double(rescale_mic(x = as.double(x), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE)) } scale$transform_df <- function(self, df) { self$`.values_rescaled` <- rescale_mic(x = as.double(df[[aest]]), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE) - self$`.values_levels` <- levels(rescale_mic(x = as.double(df[[aest]]), keep_operators = keep_operators, mic_range = mic_range, as.mic = FALSE)) - if (length(self$`.values_levels`) > 6 & "0.025" %in% self$`.values_levels`) { - # TODO weird levelling out leading to 0.025 being redundant - self$`.values_levels` <- self$`.values_levels`[self$`.values_levels` != "0.025"] + + # create new breaks and labels here + lims <- range(self$`.values_rescaled`) + if (!is.na(mic_range[1]) && mic_range[1] < lims[1]) { + lims[1] <- mic_range[1] } + if (!is.na(mic_range[2]) && mic_range[2] > lims[2]) { + lims[2] <- mic_range[2] + } + ind_min <- which(COMMON_MIC_VALUES <= lims[1])[which.min(abs(COMMON_MIC_VALUES[COMMON_MIC_VALUES <= lims[1]] - lims[1]))] # Closest index where COMMON_MIC_VALUES <= lims[1] + ind_max <- which(COMMON_MIC_VALUES >= lims[2])[which.min(abs(COMMON_MIC_VALUES[COMMON_MIC_VALUES >= lims[2]] - lims[2]))] # Closest index where COMMON_MIC_VALUES >= lims[2] + self$`.values_levels` <- as.mic(COMMON_MIC_VALUES[ind_min:ind_max]) + + if (keep_operators %in% c("edges", "all") && length(self$`.values_levels`) > 1) { + self$`.values_levels`[1] <- paste0("<=", self$`.values_levels`[1]) + self$`.values_levels`[length(self$`.values_levels`)] <- paste0(">=", self$`.values_levels`[length(self$`.values_levels`)]) + } + self$`.values_log` <- log2(as.double(self$`.values_rescaled`)) if (aest == "y" && "group" %in% colnames(df)) { df$group <- as.integer(factor(df$x)) diff --git a/data-raw/gpt_training_text_v2.1.1.9151.txt b/data-raw/gpt_training_text_v2.1.1.9152.txt similarity index 99% rename from data-raw/gpt_training_text_v2.1.1.9151.txt rename to data-raw/gpt_training_text_v2.1.1.9152.txt index 949fcfb4f..6458fb78c 100644 --- a/data-raw/gpt_training_text_v2.1.1.9151.txt +++ b/data-raw/gpt_training_text_v2.1.1.9152.txt @@ -1,6 +1,6 @@ This knowledge base contains all context you must know about the AMR package for R. You are a GPT trained to be an assistant for the AMR package in R. You are an incredible R specialist, especially trained in this package and in the tidyverse. -First and foremost, you are trained on version 2.1.1.9151. Remember this whenever someone asks which AMR package version you’re at. +First and foremost, you are trained on version 2.1.1.9152. Remember this whenever someone asks which AMR package version you’re at. Below are the contents of the file, the file, and all the files (documentation) in the package. Every file content is split using 100 hypens. ---------------------------------------------------------------------------------------------------- diff --git a/tests/testthat/test-mic.R b/tests/testthat/test-mic.R index f3fbe4b20..fcbee903c 100755 --- a/tests/testthat/test-mic.R +++ b/tests/testthat/test-mic.R @@ -27,12 +27,15 @@ # how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # ==================================================================== # +# used in multiple functions, also in plotting +expect_true(all(as.mic(COMMON_MIC_VALUES) %in% VALID_MIC_LEVELS)) +expect_true(all(paste0("<=", as.mic(COMMON_MIC_VALUES)) %in% VALID_MIC_LEVELS)) +expect_true(all(paste0(">=", as.mic(COMMON_MIC_VALUES)) %in% VALID_MIC_LEVELS)) + expect_true(as.mic(8) == as.mic("8")) expect_true(as.mic("1") > as.mic("<=0.0625")) expect_true(as.mic("1") < as.mic(">=32")) expect_true(is.mic(as.mic(8))) -# expect_true(as.mic(1024) < as.mic(">1024")) -# expect_true(as.mic("<1024") > as.mic("1024")) expect_equal(as.double(as.mic(">=32")), 32)